Crawford Revie Eva Blomqvist Karl Hammar Matthias Filter Patrick Lambrix Taras Günther Fernanda Dórea An ontology to support semantic interoperability among domains involved in health surveillance (animal health, public health and food safety). More details at http://datadrivensurveillance.org. Health Surveillance Ontology (HSO) This is an ontology to support (one) health surveillance, focused on "surveillance system level data", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. Relates an entity in the ontology to the name of the variable that is used to represent it in the code that generates the BFO OWL file from the lispy specification. Really of interest to developers only BFO OWL specification label Relates an entity in the ontology to the term that is used to represent it in the the CLIF specification of BFO2 Person:Alan Ruttenberg Really of interest to developers only BFO CLIF specification label From the European Food Safety Agency (EFSA): https://zenodo.org/record/344473#.WzvvyvkzYkV The Data Collection Framework (DCF) application is constituted of an interactive web-based application that aims at facilitating data exchange, data extraction and data reusability. A harmonized terminology is used to collect and analyse data in a coherent way with the aim to support scientific research. DCF_catalogues file contains all the valid catalogues published in the DCF. The SSD2 file contains the controlled terminologies based on the standard description of samples and analytical results (Standard Sample Description Extension), extended to cover additional data collection domains, such as zoonotic agents in food and animals, antimicrobial resistance and food additives. This annotation points to the specific catalague, within SSD2, form which terms were imported. SSD_catalogue "This annotation gives the specific code for the concept include din the ontology. Look for this code in the specific catalogue via the annotation property ""SSD_catalogue"". Full names are stored in the property ""SSD_termExtendedName""." SSD_termCode This annotation gives the specific term name for the concept include din the ontology. Look for this name in the specific catalogue via the annotation property "SSD_catalogue". Codes are stored in the property "SSD_termCode". SSD_termExtendedName This annotation gives any additional notes. Look for this name in the specific catalogue via the annotation property "SSD_catalogue". Codes are stored in the property "SSD_termCode". SSD_termScopeNote A collection of annotations which refer to all the annotation steps in the One Health Consensus Reporting Annotation Checklist (OH-CRAC). OH-CRAC is part of the One Health Codex - https://oh-surveillance-codex.readthedocs.io/en/latest/5-the-reporting-principle.html. One-Health Consensus Reference Annotation Checklist (OH-CRAC) This section provides information on what "caused" the surveillance activity and what is expected from the surveillance activity. It may be triggered by a new law or feedback from previous surveillance activities. It might even be initiated by practices in other (national and international) organisations. CRAC 1.1 Motivation / cause This section documents the results of consultation activities between the surveillance "actor" with its customers / stakeholders to identify/confirm the needs of the surveillance activity. Specifically, it documents what is agreed to be delivered by this surveillance activity, when, how and why. It also documents whether previously identified needs have changed. CRAC 1.2. Requirement analysis This section documents what surveillance objectives (e.g. prevalence estimation, case detection, early detection, disease freedom) and their quality criteria are defined to meet the needs of the end-users / stakeholders. It also describes existing legal or practical constraints, e.g. confidentiality, resources etc. CRAC 1.3. Surveillance objective and constraints This section gives an overview on all designed outputs, products and services related to the surveillance activity. This includes the output of the surveillance activity, but also related work, as e.g. preparation of systems and tools for dissemination, disclosure control methods etc. CRAC 2.1. Framework design This section describes which variables / measurements were planned to be collected / taken and which metadata set / standard were used. It further specifies if measured values were planned to be grouped or classified, how this was planned to be done. It also specifies if new variables derive from the original ones (see section 4.5, New variable/unit derivation). It may overlap with the description requested for section 2.3 (Surveillance methods/strategy) CRAC 2.2. Variable specifications This section describes the developed "collection strategy" (collection strategy in this context means, e.g. active or passive surveillance). It also describes the collection instruments (survey, data extraction methods etc.) and collection units (e.g. individuals, herds, food batch etc.). It may overlap with the surveillance variables specification described in section 2.2 (Variable specifications) CRAC 2.3. Surveillance methods/strategy CRAC 2.4. Sampling plan "This sub-section specifies the population(s) that were sampled. " CRAC 2.4.1. Sampled population This sub-section describes the design process followed for the sampling plan generation and the sampling criteria. CRAC 2.4.2. Sampling schema This sub-section describes the sample collection approach carried out including information on the practical handling, storage and labeling of taken samples by different actors (e.g. storage temperature, labeling with unique IDs). CRAC 2.4.3. Sample collection This sub-section details the processing of the samples prior to the analytical processing. CRAC 2.4.4. Sample preparation This sub-section reports on the analytical procedures applied to the different sets of samples. CRAC 2.4.5. Analytical procedures This section describes the methods used for the data processing including analysis of bioinformatics, trends, modelling, statistical tests, etc. This section also includes design of specifications for data integration from multiple data sources, validation of data and estimation. CRAC 2.5. Data processing/analysis This section describes how the specific sampling units were chosen based on the sampling plan that is described in section 2.4 (Sampling plan). In contrast to the information given in 2.4, this section should describe how the real "implementation" of the sampling plan took place, as sometimes the "field work" is done by other actors than the planning. CRAC 3.1. Practical aspects on sample selection "This section describes the activies undertaken to ensure that the people, processes and technology (e.g. web-based applications, GPS system) were ready to collect data and metadata. It includes the strategy, planning and training activities in preparation for the specific sampling activity. This description might include information on: - Preparing a sample storage and / or shipment strategy; - Training staff how to collect samples, e.g. physician; - Training staff how to analyze selected samples in the lab, e.g. perform ring trials - Provisioning of collection resources (e.g. laptops, collection apps, central data or sample repositories, questionnaires, information leaflets or letters, required lab material); - Agreements with intermediate collection bodies, (e.g. sub-contractors); - How security and confidentiality of data to be collected and data transmission was guaranteed" CRAC 3.2. Practical support activities This section describes how the execution / implementation of the sample collection worked out, e.g. if there were corrective actions taken along the sampling period. This should include reports on quality control activities carried out by labs and actors involved in sample collection. CRAC 3.3. Practical aspects on field and lab work "This section describes how the collected lab data and metadata were loaded into a suitable electronic environment for further processing. It may include a description of manual or automatic data capture processes that were applied to extract e.g. metadata from paper questionnaires, or converting the formats of files or encoding the variables received. It may also include analysis of the metadata and paradata associated with collection to ensure the collection activities have met requirements. It might also describe how physical samples or related material (questionnaires) will be archived. When software is used for data collection the version and software archiving should be described." CRAC 3.4. Practical aspects on information handling "This section describes any activity related to data integration or data fusion. The data collection could be a combination of new and historical data, from external or internal sources, from a variety of collection instruments etc. For example the data collection could be enriched by information from official (governmental) or non-official sources. It could further include a description on: - Data pooling, with the aim of increasing the effective number of observations of some phenomena; - Mapping or record linkage routines, with the aim of linking different data sources that use different encoding schemas; - Prioritising, when two or more sources contain data for the same variable, with potentially different values. - Data anonymization, e.g. if identifiers such as name and address are stripped to help to protect confidentiality." CRAC 4.1. Data integration "This section describes if data/variables were classified and/or encoded. Examples: - Automatic coding routines that assign numeric codes to text responses according to a pre-determined statistical classification. - Classification based on analytical results (e.g. MLST pattern), bioinformatics analysis (e.g. phylogenetic trees) or mathematical models (PCA, SVM / ANN)" CRAC 4.2. Data classification / encoding This section describes activities carried out to detect and localise actual or potential errors and discrepancies such as outliers, item non-response and miscoding (input data validation). CRAC 4.3. Data validation "This section describes what action was taken for incorrect, missing, unreliable or outdated data. For example new values may have been inserted or outdated data may have been removed. It should describe whether data were added or changed, the method used, and the flags used to mark them as changed. " CRAC 4.4. Data cleansing and correction This section describes if new data were derived from variables/units that were not explicitly provided in the data collection but were needed to deliver the required outputs. Examples include deriving variables on households where the collection units are persons or deriving variables on enterprises where the collection units are legal units. CRAC 4.5. New variable/unit derivation This section describes if weights for unit data records were created according to the methodology developed in sub-process 2.5 (Data processing/analysis). For example, weights might have been used to "gross-up" data to make them representative of the target population (e.g. for sample surveys or extracts from scanner data), or to adjust for non-response in total enumerations. In other situations, variables might have needed weighting for normalisation purpose or for benchmarking indicators (e.g. known population totals). CRAC 4.6. Weighing of records This section describes how aggregate data and population totals were generated from the data collection or lower-level aggregates. It includes summing data for records sharing certain characteristics (e.g. aggregation of data by demographic or geographic classifications), determining measures of average and dispersion, and applying weights from sub-process 4.6 (Weighting of records) to derive appropriate totals. In the case of statistical outputs, which use sample surveys, sampling errors corresponding to relevant aggregates may also be calculated in this section. CRAC 4.7. Data aggregation This section describes how data from section 4.7 (Data aggregation) were transformed into surveillance statistics outputs such as indexes, seasonally adjusted statistics, e.g. trend, cycle, seasonal and irregular components, accessibility measures, etc., as well as the recording of quality characteristics such as coefficients of variation. The preparation of maps, GIS outputs and geo-statistical services can be included to maximise the value and capacity to analyse the statistical information. CRAC 5.1. Surveillance output generation "This section describes how the quality of the generated surveillance statistical outputs were validated, in accordance with a general quality framework and with expectations. Validation activities can include: - Checking that the population coverage and response rates are as required; - Comparing the statistics with previous cycles (if applicable); - Checking that the associated metadata, paradata and quality indicators are present and in line with expectations; - Checking geospatial consistency of the data; - Confronting the statistics against other relevant data (both internal and external); - Investigating inconsistencies in the statistics; - Performing macro editing; - Validating the statistics against expectations and domain intelligence." CRAC 5.2. Surveillance output validation This section describes performed in-depth statistical analyses such as time-series analysis, consistency and comparability analysis, revision analysis (analysis of the differences between preliminary and revised estimates), analysis of asymmetries (discrepancies in mirror statistics) etc. CRAC 5.3. Surveillance output statistical analysis This section describes activities carried out to ensure that the data (and metadata) to be disseminated do not breach the appropriate rules on confidentiality according to either organisation policies and rules, or to the process-specific methodology created in section 2.5 (Data processing/analysis plan). This may include checks for primary and secondary disclosure, as well as the application of data suppression or perturbation techniques and output checking. The degree and method of statistical disclosure control may vary for different types of outputs. For example, the approach used for microdata sets for research purposes will be different to that for published tables, finalised outputs of geospatial statistics or visualisations on maps. CRAC 5.4. Surveillance disclosure control annotations created to map specific entities to their origin in the Standard Sample Description, a terminology catalogue maintained by the European Foos Safety Agency (EFSA). https://www.efsa.europa.eu/en/efsajournal/pub/3424 European Food Safety Agency Standard Sample Description Framework - EFSA SSD surveillance output discussion Annotation property created to be a "catch all" property for information given about a surveillance activity, and not recognized as any specific entity in the ontology when using automated RDF conversion/import tools. additional information editor preferred term example of usage definition definition editor note term editor alternative term definition source curator note imported from elucidation has associated axiom(nl) has associated axiom(fol) has axiom label A metadata relation between a class and its taxonomic rank (eg species, family) ncbi_taxonomy This is an abstract class for use with the NCBI taxonomy to name the depth of the node within the tree. The link between the node term and the rank is only visible if you are using an obo 1.3 aware browser/editor; otherwise this can be ignored has_rank has_alternative_id has broad synonym has_broad_synonym database_cross_reference has exact synonym has_exact_synonym has narrow synonym has_narrow_synonym has_obo_namespace has_related_synonym has synonym From the European Food Safety Agency (EFSA): https://zenodo.org/record/344473#.WzvvyvkzYkV The Data Collection Framework (DCF) application is constituted of an interactive web-based application that aims at facilitating data exchange, data extraction and data reusability. A harmonized terminology is used to collect and analyse data in a coherent way with the aim to support scientific research. DCF_catalogues file contains all the valid catalogues published in the DCF. The SSD2 file contains the controlled terminologies based on the standard description of samples and analytical results (Standard Sample Description Extension), extended to cover additional data collection domains, such as zoonotic agents in food and animals, antimicrobial resistance and food additives. This annotation points to the specific catalague, within SSD2, form which terms were imported. SSD_catalogue "This annotation gives the specific code for the concept include din the ontology. Look for this code in the specific catalogue via the annotation property ""SSD_catalogue"". Full names are stored in the property ""SSD_termExtendedName""." SSD_termCode This annotation gives the specific term name for the concept include din the ontology. Look for this name in the specific catalogue via the annotation property "SSD_catalogue". Codes are stored in the property "SSD_termCode". SSD_termExtendedName This annotation gives any additional notes. Look for this name in the specific catalogue via the annotation property "SSD_catalogue". Codes are stored in the property "SSD_termCode". SSD_termScopeNote A collection of annotations which refer to all the annotation steps in the One Health Consensus Reporting Annotation Checklist (OH-CRAC). OH-CRAC is part of the One Health Codex - https://oh-surveillance-codex.readthedocs.io/en/latest/5-the-reporting-principle.html. One-Health Consensus Reference Annotation Checklist (OH-CRAC) This section provides information on what "caused" the surveillance activity and what is expected from the surveillance activity. It may be triggered by a new law or feedback from previous surveillance activities. It might even be initiated by practices in other (national and international) organisations. CRAC 1.1 Motivation / cause This section documents the results of consultation activities between the surveillance "actor" with its customers / stakeholders to identify/confirm the needs of the surveillance activity. Specifically, it documents what is agreed to be delivered by this surveillance activity, when, how and why. It also documents whether previously identified needs have changed. CRAC 1.2. Requirement analysis This section documents what surveillance objectives (e.g. prevalence estimation, case detection, early detection, disease freedom) and their quality criteria are defined to meet the needs of the end-users / stakeholders. It also describes existing legal or practical constraints, e.g. confidentiality, resources etc. CRAC 1.3. Surveillance objective and constraints This section gives an overview on all designed outputs, products and services related to the surveillance activity. This includes the output of the surveillance activity, but also related work, as e.g. preparation of systems and tools for dissemination, disclosure control methods etc. CRAC 2.1. Framework design This section describes which variables / measurements were planned to be collected / taken and which metadata set / standard were used. It further specifies if measured values were planned to be grouped or classified, how this was planned to be done. It also specifies if new variables derive from the original ones (see section 4.5, New variable/unit derivation). It may overlap with the description requested for section 2.3 (Surveillance methods/strategy) CRAC 2.2. Variable specifications This section describes the developed "collection strategy" (collection strategy in this context means, e.g. active or passive surveillance). It also describes the collection instruments (survey, data extraction methods etc.) and collection units (e.g. individuals, herds, food batch etc.). It may overlap with the surveillance variables specification described in section 2.2 (Variable specifications) CRAC 2.3. Surveillance methods/strategy CRAC 2.4. Sampling plan "This sub-section specifies the population(s) that were sampled. " CRAC 2.4.1. Sampled population This sub-section describes the design process followed for the sampling plan generation and the sampling criteria. CRAC 2.4.2. Sampling schema This sub-section describes the sample collection approach carried out including information on the practical handling, storage and labeling of taken samples by different actors (e.g. storage temperature, labeling with unique IDs). CRAC 2.4.3. Sample collection This sub-section details the processing of the samples prior to the analytical processing. CRAC 2.4.4. Sample preparation This sub-section reports on the analytical procedures applied to the different sets of samples. CRAC 2.4.5. Analytical procedures This section describes the methods used for the data processing including analysis of bioinformatics, trends, modelling, statistical tests, etc. This section also includes design of specifications for data integration from multiple data sources, validation of data and estimation. CRAC 2.5. Data processing/analysis This section describes how the specific sampling units were chosen based on the sampling plan that is described in section 2.4 (Sampling plan). In contrast to the information given in 2.4, this section should describe how the real "implementation" of the sampling plan took place, as sometimes the "field work" is done by other actors than the planning. CRAC 3.1. Practical aspects on sample selection "This section describes the activies undertaken to ensure that the people, processes and technology (e.g. web-based applications, GPS system) were ready to collect data and metadata. It includes the strategy, planning and training activities in preparation for the specific sampling activity. This description might include information on: - Preparing a sample storage and / or shipment strategy; - Training staff how to collect samples, e.g. physician; - Training staff how to analyze selected samples in the lab, e.g. perform ring trials - Provisioning of collection resources (e.g. laptops, collection apps, central data or sample repositories, questionnaires, information leaflets or letters, required lab material); - Agreements with intermediate collection bodies, (e.g. sub-contractors); - How security and confidentiality of data to be collected and data transmission was guaranteed" CRAC 3.2. Practical support activities This section describes how the execution / implementation of the sample collection worked out, e.g. if there were corrective actions taken along the sampling period. This should include reports on quality control activities carried out by labs and actors involved in sample collection. CRAC 3.3. Practical aspects on field and lab work "This section describes how the collected lab data and metadata were loaded into a suitable electronic environment for further processing. It may include a description of manual or automatic data capture processes that were applied to extract e.g. metadata from paper questionnaires, or converting the formats of files or encoding the variables received. It may also include analysis of the metadata and paradata associated with collection to ensure the collection activities have met requirements. It might also describe how physical samples or related material (questionnaires) will be archived. When software is used for data collection the version and software archiving should be described." CRAC 3.4. Practical aspects on information handling "This section describes any activity related to data integration or data fusion. The data collection could be a combination of new and historical data, from external or internal sources, from a variety of collection instruments etc. For example the data collection could be enriched by information from official (governmental) or non-official sources. It could further include a description on: - Data pooling, with the aim of increasing the effective number of observations of some phenomena; - Mapping or record linkage routines, with the aim of linking different data sources that use different encoding schemas; - Prioritising, when two or more sources contain data for the same variable, with potentially different values. - Data anonymization, e.g. if identifiers such as name and address are stripped to help to protect confidentiality." CRAC 4.1. Data integration "This section describes if data/variables were classified and/or encoded. Examples: - Automatic coding routines that assign numeric codes to text responses according to a pre-determined statistical classification. - Classification based on analytical results (e.g. MLST pattern), bioinformatics analysis (e.g. phylogenetic trees) or mathematical models (PCA, SVM / ANN)" CRAC 4.2. Data classification / encoding This section describes activities carried out to detect and localise actual or potential errors and discrepancies such as outliers, item non-response and miscoding (input data validation). CRAC 4.3. Data validation "This section describes what action was taken for incorrect, missing, unreliable or outdated data. For example new values may have been inserted or outdated data may have been removed. It should describe whether data were added or changed, the method used, and the flags used to mark them as changed. " CRAC 4.4. Data cleansing and correction This section describes if new data were derived from variables/units that were not explicitly provided in the data collection but were needed to deliver the required outputs. Examples include deriving variables on households where the collection units are persons or deriving variables on enterprises where the collection units are legal units. CRAC 4.5. New variable/unit derivation This section describes if weights for unit data records were created according to the methodology developed in sub-process 2.5 (Data processing/analysis). For example, weights might have been used to "gross-up" data to make them representative of the target population (e.g. for sample surveys or extracts from scanner data), or to adjust for non-response in total enumerations. In other situations, variables might have needed weighting for normalisation purpose or for benchmarking indicators (e.g. known population totals). CRAC 4.6. Weighing of records This section describes how aggregate data and population totals were generated from the data collection or lower-level aggregates. It includes summing data for records sharing certain characteristics (e.g. aggregation of data by demographic or geographic classifications), determining measures of average and dispersion, and applying weights from sub-process 4.6 (Weighting of records) to derive appropriate totals. In the case of statistical outputs, which use sample surveys, sampling errors corresponding to relevant aggregates may also be calculated in this section. CRAC 4.7. Data aggregation This section describes how data from section 4.7 (Data aggregation) were transformed into surveillance statistics outputs such as indexes, seasonally adjusted statistics, e.g. trend, cycle, seasonal and irregular components, accessibility measures, etc., as well as the recording of quality characteristics such as coefficients of variation. The preparation of maps, GIS outputs and geo-statistical services can be included to maximise the value and capacity to analyse the statistical information. CRAC 5.1. Surveillance output generation "This section describes how the quality of the generated surveillance statistical outputs were validated, in accordance with a general quality framework and with expectations. Validation activities can include: - Checking that the population coverage and response rates are as required; - Comparing the statistics with previous cycles (if applicable); - Checking that the associated metadata, paradata and quality indicators are present and in line with expectations; - Checking geospatial consistency of the data; - Confronting the statistics against other relevant data (both internal and external); - Investigating inconsistencies in the statistics; - Performing macro editing; - Validating the statistics against expectations and domain intelligence." CRAC 5.2. Surveillance output validation This section describes performed in-depth statistical analyses such as time-series analysis, consistency and comparability analysis, revision analysis (analysis of the differences between preliminary and revised estimates), analysis of asymmetries (discrepancies in mirror statistics) etc. CRAC 5.3. Surveillance output statistical analysis This section describes activities carried out to ensure that the data (and metadata) to be disseminated do not breach the appropriate rules on confidentiality according to either organisation policies and rules, or to the process-specific methodology created in section 2.5 (Data processing/analysis plan). This may include checks for primary and secondary disclosure, as well as the application of data suppression or perturbation techniques and output checking. The degree and method of statistical disclosure control may vary for different types of outputs. For example, the approach used for microdata sets for research purposes will be different to that for published tables, finalised outputs of geospatial statistics or visualisations on maps. CRAC 5.4. Surveillance disclosure control annotations created to map specific entities to their origin in the Standard Sample Description, a terminology catalogue maintained by the European Foos Safety Agency (EFSA). https://www.efsa.europa.eu/en/efsajournal/pub/3424 European Food Safety Agency Standard Sample Description Framework - EFSA SSD surveillance output discussion Annotation property created to be a "catch all" property for information given about a surveillance activity, and not recognized as any specific entity in the ontology when using automated RDF conversion/import tools. additional information is part of my brain is part of my body (continuant parthood, two material entities) my stomach cavity is part of my stomach (continuant parthood, immaterial entity is part of material entity) this day is part of this year (occurrent parthood) a core relation that holds between a part and its whole Everything is part of itself. Any part of any part of a thing is itself part of that thing. Two distinct things cannot be part of each other. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent can be part of an occurrent; only a process can be part of a process; only a continuant can be part of a continuant; only an independent continuant can be part of an independent continuant; only an immaterial entity can be part of an immaterial entity; only a specifically dependent continuant can be part of a specifically dependent continuant; only a generically dependent continuant can be part of a generically dependent continuant. (This list is not exhaustive.) A continuant cannot be part of an occurrent: use 'participates in'. An occurrent cannot be part of a continuant: use 'has participant'. A material entity cannot be part of an immaterial entity: use 'has location'. A specifically dependent continuant cannot be part of an independent continuant: use 'inheres in'. An independent continuant cannot be part of a specifically dependent continuant: use 'bearer of'. part_of BFO:0000050 uberon part_of part_of part of part of http://www.obofoundry.org/ro/#OBO_REL:part_of realized in this disease is realized in this disease course this fragility is realized in this shattering this investigator role is realized in this investigation is realized by realized_in [copied from inverse property 'realizes'] to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a realizable entity and a process, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realized in realizes this disease course realizes this disease this investigation realizes this investigator role this shattering realizes this fragility to say that b realizes c at t is to assert that there is some material entity d & b is a process which has participant d at t & c is a disposition or role of which d is bearer_of at t& the type instantiated by b is correlated with the type instantiated by c. (axiom label in BFO2 Reference: [059-003]) Paraphrase of elucidation: a relation between a process and a realizable entity, where there is some material entity that is bearer of the realizable entity and participates in the process, and the realizable entity comes to be realized in the course of the process realizes X preceded_by Y iff: end(Y) before_or_simultaneous_with start(X) BFO:0000062 is preceded by takes place after uberon preceded_by preceded_by preceded_by BFO:0000063 uberon precedes precedes precedes x anterior_to y iff x is further along the antero-posterior axis than y, towards the head. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail: bearer cjm 2009-07-31T02:15:46Z BSPO:0000096 uberon anterior_to anterior_to anterior_to x distal_to y iff x is further along the proximo-distal axis than y, towards the appendage tip. A proximo-distal axis extends from tip of an appendage (distal) to where it joins the body (proximal). BSPO:0000097 uberon distal_to distal_to distal_to x dorsal_to y iff x is further along the dorso-ventral axis than y, towards the back. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000098 uberon dorsal_to dorsal_to dorsal_to x posterior_to y iff x is further along the antero-posterior axis than y, towards the body/tail. An antero-posterior axis is an axis that bisects an organism from head end to opposite end of body or tail. BSPO:0000099 caudal_to uberon posterior_to posterior_to posterior_to x ventral_to y iff x is further along the dorso-ventral axis than y, towards the front. A dorso-ventral axis is an axis that bisects an organism from back (e.g. spinal column) to front (e.g. belly). BSPO:0000102 uberon ventral_to ventral_to ventral_to Further away from the surface of the organism. Thus, the muscular layer is deep to the skin, but superficial to the intestines. BSPO:0000107 uberon deep_to deep_to deep_to Near the outer surface of the organism. Thus, skin is superficial to the muscle layer. BSPO:0000108 uberon superficial_to superficial_to superficial_to X proximal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the proximal portion. BSPO:0000124 uberon in_proximal_side_of in_proximal_side_of in_proximal_side_of X distal_side_of Y <=> if Y is subdivided into distal and proximal portions, X is part_of the distal portion. BSPO:0000125 uberon in_distal_side_of in_distal_side_of in_distal_side_of isSubSpeciesOf isSerotypeOf has datum has specimen datum has matrix type sampled from sampled from anatomical entity sampled from organism has specimen from organism type follows surveillance protocol excuted in surveillance activity has legal basis is legal basis of has surveillance objective has surveillance purpose has surveillance actions has sampling design has reporting protocol has sample collection protocol has diagnostic protocol has surveillance context target population target geographical area target country target host species target host sector Mixed outbreaks target pathogen causative agent susceptible species Specification of the type of sampling strategy planned within a surveillance protocol, and ultimately executed in a surveillance activity. applies sampling strategy has sampling unit has sampler type sampling stage sampled specimen employs assay property assigning specific datum to diagnostic tests which allows identification of their type has diagnostic test type assignment of data available as information content to assays has assay datum reporting country origin country this property allows metadata documentation to link a dataset to specific entities within each and vice-versa, as long as these entitites ave unique URI, even when the dataset is not itself available as linked data this property allows a dataset to be explictly linked to any entities within it which can be referred to with an unique ID. contains information about this property allows metadata documentation to link a dataset to specific entities within each and vice-versa, as long as these entitites ave unique URI, even when the dataset is not itself available as linked data Links an entityt to a specific dataset that contains information about it. documented in dataset this property specifies specifically whic country is responsible for the documentation about a specific surveillance activity reporting country available in language place of exposure place of origin of the problem hazard status context is_specified_input_of some Autologous EBV(Epstein-Barr virus)-transformed B-LCL (B lymphocyte cell line) is_input_for instance of Chromum Release Assay described at https://wiki.cbil.upenn.edu/obiwiki/index.php/Chromium_Release_assay A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_input_of achieves_planned_objective A cell sorting process achieves the objective specification 'material separation objective' This relation obtains between a planned process and a objective specification when the criteria specified in the objective specification are met at the end of the planned process. BP, AR, PPPB branch PPPB branch derived modified according to email thread from 1/23/09 in accordince with DT and PPPB branch achieves_planned_objective objective_achieved_by This relation obtains between an objective specification and a planned process when the criteria specified in the objective specification are met at the end of the planned process. OBI OBI objective_achieved_by inheres in this fragility inheres in this vase this red color inheres in this apple a relation between a specifically dependent continuant (the dependent) and an independent continuant (the bearer), in which the dependent specifically depends on the bearer for its existence A dependent inheres in its bearer at all times for which the dependent exists. inheres_in inheres in bearer of this apple is bearer of this red color this vase is bearer of this fragility a relation between an independent continuant (the bearer) and a specifically dependent continuant (the dependent), in which the dependent specifically depends on the bearer for its existence A bearer can have many dependents, and its dependents can exist for different periods of time, but none of its dependents can exist when the bearer does not exist. bearer_of is bearer of bearer of participates in this blood clot participates in this blood coagulation this input material (or this output material) participates in this process this investigator participates in this investigation a relation between a continuant and a process, in which the continuant is somehow involved in the process participates_in participates in has participant this blood coagulation has participant this blood clot this investigation has participant this investigator this process has participant this input material (or this output material) a relation between a process and a continuant, in which the continuant is somehow involved in the process Has_participant is a primitive instance-level relation between a process, a continuant, and a time at which the continuant participates in some way in the process. The relation obtains, for example, when this particular process of oxygen exchange across this particular alveolar membrane has_participant this particular sample of hemoglobin at this particular time. has_participant http://www.obofoundry.org/ro/#OBO_REL:has_participant has participant A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The journal article (a generically dependent continuant) is concretized as the quality (a specifically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a generically dependent continuant and a specifically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. A generically dependent continuant may be concretized as multiple specifically dependent continuants. is concretized as A journal article is an information artifact that inheres in some number of printed journals. For each copy of the printed journal there is some quality that carries the journal article, such as a pattern of ink. The quality (a specifically dependent continuant) concretizes the journal article (a generically dependent continuant), and both depend on that copy of the printed journal (an independent continuant). An investigator reads a protocol and forms a plan to carry out an assay. The plan is a realizable entity (a specifically dependent continuant) that concretizes the protocol (a generically dependent continuant), and both depend on the investigator (an independent continuant). The plan is then realized by the assay (a process). A relationship between a specifically dependent continuant and a generically dependent continuant, in which the generically dependent continuant depends on some independent continuant in virtue of the fact that the specifically dependent continuant also depends on that same independent continuant. Multiple specifically dependent continuants can concretize the same generically dependent continuant. concretizes this catalysis function is a function of this enzyme a relation between a function and an independent continuant (the bearer), in which the function specifically depends on the bearer for its existence A function inheres in its bearer at all times for which the function exists, however the function need not be realized at all the times that the function exists. function_of is function of function of this red color is a quality of this apple a relation between a quality and an independent continuant (the bearer), in which the quality specifically depends on the bearer for its existence A quality inheres in its bearer at all times for which the quality exists. is quality of quality_of quality of this investigator role is a role of this person a relation between a role and an independent continuant (the bearer), in which the role specifically depends on the bearer for its existence A role inheres in its bearer at all times for which the role exists, however the role need not be realized at all the times that the role exists. is role of role_of role of this person has role this investigator role (more colloquially: this person has this role of investigator) a relation between an independent continuant (the bearer) and a role, in which the role specifically depends on the bearer for its existence A bearer can have many roles, and its roles can exist for different periods of time, but none of its roles can exist when the bearer does not exist. A role need not be realized at all the times that the role exists. has_role has role disposition of derives from this cell derives from this parent cell (cell division) this nucleus derives from this parent nucleus (nuclear division) a relation between two distinct material entities, the new entity and the old entity, in which the new entity begins to exist when the old entity ceases to exist, and the new entity inherits the significant portion of the matter of the old entity This is a very general relation. More specific relations are preferred when applicable, such as 'directly develops from'. derives_from derives from RO:0001015 uberon location_of location_of location_of RO:0002002 uberon has_boundary has_boundary has boundary Relation between occurrents, shares start and end boundaries. RO:0002082 coincides_with is_equal_to uberon simultaneous_with simultaneous_with simultaneous_with X immediately_preceded_by Y iff: end(X) simultaneous_with start(Y) A non-transitive temporal relation in which one process immediately precedes another process, such that there is no interval of time between the two processes[SIO:000251]. RO:0002087 directly preceded by is directly preceded by is immediately preceded by starts_at_end_of uberon immediately_preceded_by immediately_preceded_by immediately_preceded_by RO:0002150 uberon continuous_with continuous_with continuous_with Binary relationship: x connected_to y if and only if there exists some z such that z connects x and y in a ternary connected_to(x,y,z) relationship. RO:0002170 uberon connected_to connected_to Connection does not imply overlaps. connected to Binary relationship: z connects x if and only if there exists some y such that z connects x and y in a ternary connected_to(x,y,z) relationship. this is currently used for both structural relationships (such as between a valve and the chamber it connects) and abstract relationships (anatomical lines and the entities they connect) RO:0002176 uberon connects connects connects relation between an artery and the structure is supplies with blood. RO:0002178 arterial supply of uberon supplies supplies source: FMA supplies RO:0002202 uberon develops_from develops_from develops_from RO:0002203 uberon develops_into develops_into develops_into x surrounded_by y iff: x is adjacent to y and for every region r adjacent to x, r overlaps y RO:0002219 uberon surrounded_by surrounded_by surrounded_by x adjacent_to y iff: x and y share a boundary RO:0002220 uberon adjacent_to adjacent_to adjacent_to inverse of surrounded_by RO:0002221 uberon surrounds surrounds surrounds Relation between occurrents, shares a start boundary with. RO:0002223 uberon starts starts starts RO:0002224 uberon starts_with starts_with starts with Relation between occurrents, shares an end boundary with. RO:0002229 finishes uberon ends ends ends RO:0002230 uberon ends_with ends_with ends with RO:0002254 uberon has_developmental_contribution_from has_developmental_contribution_from has developmental contribution from t1 developmentally_induced_by t2 if there is a process of organ induction (GO:0001759) with t1 and t2 as interacting participants. t2 causes t1 to change its fate from a precursor tissue type T to T', where T' develops_from T. RO:0002256 uberon developmentally_induced_by developmentally_induced_by sources for developmentally_induced_by relationships in Uberon: Developmental Biology, Gilbert, 8th edition, figure 6.5(F) developmentally_induced_by RO:0002258 uberon developmentally_preceded_by developmentally_preceded_by developmentally preceded by RO:0002285 uberon developmentally_replaces developmentally_replaces developmentally_replaces x has potential to developmentrally contribute to y iff x developmentally contributes to y or x is capable of developmentally contributing to y RO:0002385 uberon has_potential_to_developmentally_contribute_to has_potential_to_developmentally_contribute_to has potential to developmentally contribute to x has the potential to develop into y iff x develops into y or if x is capable of developing into y RO:0002387 uberon has_potential_to_develop_into has_potential_to_develop_into has potential to develop into Relation between continuant c and occurrent s, such that every instance of c comes into existing during some s. RO:0002488 begins_to_exist_during uberon existence_starts_during existence_starts_during existence starts during Relation between continuant and occurrent, such that c comes into existence at the start of p. RO:0002489 uberon existence_starts_with existence_starts_with existence starts with Relation between continuant c and occurrent s, such that every instance of c ceases to exist during some s, if it does not die prematurely. RO:0002492 ceases_to_exist_during uberon existence_ends_during existence_ends_during existence ends during Relation between continuant and occurrent, such that c ceases to exist at the end of p. RO:0002493 uberon existence_ends_with existence_ends_with existence ends with RO:0002495 direct_transformation_of immediately transforms from uberon immediate_transformation_of immediate_transformation_of immediate transformation of RO:0002496 uberon existence_starts_during_or_after existence_starts_during_or_after existence starts during or after RO:0002497 uberon existence_ends_during_or_before existence_ends_during_or_before existence ends during or before A relation between a subdivision of an organism and the single subdivision of skeleton that provides structural support for that subdivision. RO:0002551 uberon has sekeletal support has supporting framework has_skeleton has_skeleton has skeleton RO:0002572 uberon luminal_space_of luminal_space_of luminal space of RO:0002576 uberon skeleton_of skeleton_of skeleton of carries uberon channel_for channel for uberon channels_from channels_from uberon channels_into channels_into uberon existence_starts_and_ends_during existence starts and ends during uberon extends_fibers_into extends_fibers_into Relationship between a fluid and a material entity, where the fluid is the output of a realization of a filtration role that inheres in the material entity. uberon filtered_through Relationship between a fluid and a filtration barrier, where the portion of fluid arises as a transformation of another portion of fluid on the other side of the barrier, with larger particles removed filtered through X in_central_side Y <=> if Y is subdivided into left and right portions around some median divisor, all parts of X are closer to the median divisor than the outermost lateral sides. uberon in_central_side_of in_central_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern x proximally_connected_to y iff the proximal part of x is connected to y. i.e. x connected_to y and x distal_to y. uberon proximally_connected_to proximally connected to uberon subdivision_of placeholder relation. X = 'subdivision of A' and subdivision_of some B means that X is the mereological sum of A and B subdivision of uberon transitively_connected_to transitively_connected to . uberon transitively_proximally_connected_to transitively proximally connected to isSubSpeciesOf isSerotypeOf has datum has specimen datum has matrix type sampled from sampled from anatomical entity sampled from organism has specimen from organism type follows surveillance protocol excuted in surveillance activity has legal basis is legal basis of has surveillance objective has surveillance purpose has surveillance actions has sampling design has reporting protocol has sample collection protocol has diagnostic protocol has surveillance context target population target geographical area target country target host species target host sector Mixed outbreaks target pathogen causative agent susceptible species Specification of the type of sampling strategy planned within a surveillance protocol, and ultimately executed in a surveillance activity. applies sampling strategy has sampling unit has sampler type sampling stage sampled specimen employs assay property assigning specific datum to diagnostic tests which allows identification of their type has diagnostic test type assignment of data available as information content to assays has assay datum reporting country origin country this property allows metadata documentation to link a dataset to specific entities within each and vice-versa, as long as these entitites ave unique URI, even when the dataset is not itself available as linked data this property allows a dataset to be explictly linked to any entities within it which can be referred to with an unique ID. contains information about this property allows metadata documentation to link a dataset to specific entities within each and vice-versa, as long as these entitites ave unique URI, even when the dataset is not itself available as linked data Links an entityt to a specific dataset that contains information about it. documented in dataset this property specifies specifically whic country is responsible for the documentation about a specific surveillance activity reporting country available in language place of exposure place of origin of the problem hazard status context surveillance activity history item surveillance activity start date surveillance activity end date Number of units tested Number of PSU tested Number of SSU tested Number of units positive Number of PSU positive Number of SSU positive Number of units negative Number of PSU negative Number of SSU negative Number of specimen tested Number of specimen negative The sample size calculated for a surveillance activity in order to achieve its specific surveillance purpose or goal, and considering its declared epidemiological unit. calculated sample size The number of herds to be sampled in a survey targetting livestock animals, which are kept in herds. In a sampling process targetting clustered units, this refers to the number of PRIMARY SAMPLING UNITS to be sampled, according to the plan designed for a surveillance activity in order to achieve its specific surveillance purpose or goal. calculated number of PSU The number of animals to be sampled within each herd. In a sampling process targetting clustered units, this refers to the number of SECONDARY SAMPLING UNITS to be sampled, according to the plan designed for a surveillance activity in order to achieve its specific surveillance purpose or goal. calculated number of SSU Number of specimen positive 0.0 100.0 Percentage of units positive 0.0 100.0 Percentage of PSU positive 0.0 100.0 Percentage of SSU positive 0.0 100.0 percentage of specimen positive a collection of properties used to assign numeric results to a surveillance activity surveillance activity aggregated results surveillance activity year year started Number of cases Number of domestic cases Number of imported cases the weight of a specific collected specimen. use sub-properties to specify weight units specimen weight the weight of a specific collected specimen, in grams sampling weight in grams the weight of a specific collected specimen, in mililitres sampling weight in millilitre The case-fatality rate is the proportion of persons with a particular condition (cases) who die from that condition. It is a measure of the severity of the condition. https://www.cdc.gov/csels/dsepd/ss1978/lesson3/section3.html Case fatality rate Hospitalized cases Notification rate Notification rate in domestic cases Number of deaths case definition surveillance activity history item surveillance activity start date surveillance activity end date Number of units tested Number of PSU tested Number of SSU tested Number of units positive Number of PSU positive Number of SSU positive Number of units negative Number of PSU negative Number of SSU negative Number of specimen tested Number of specimen negative The sample size calculated for a surveillance activity in order to achieve its specific surveillance purpose or goal, and considering its declared epidemiological unit. calculated sample size The number of herds to be sampled in a survey targetting livestock animals, which are kept in herds. In a sampling process targetting clustered units, this refers to the number of PRIMARY SAMPLING UNITS to be sampled, according to the plan designed for a surveillance activity in order to achieve its specific surveillance purpose or goal. calculated number of PSU The number of animals to be sampled within each herd. In a sampling process targetting clustered units, this refers to the number of SECONDARY SAMPLING UNITS to be sampled, according to the plan designed for a surveillance activity in order to achieve its specific surveillance purpose or goal. calculated number of SSU Number of specimen positive 0.0 100.0 Percentage of units positive 0.0 100.0 Percentage of PSU positive 0.0 100.0 Percentage of SSU positive 0.0 100.0 percentage of specimen positive a collection of properties used to assign numeric results to a surveillance activity surveillance activity aggregated results surveillance activity year year started Number of cases Number of domestic cases Number of imported cases the weight of a specific collected specimen. use sub-properties to specify weight units specimen weight the weight of a specific collected specimen, in grams sampling weight in grams the weight of a specific collected specimen, in mililitres sampling weight in millilitre The case-fatality rate is the proportion of persons with a particular condition (cases) who die from that condition. It is a measure of the severity of the condition. https://www.cdc.gov/csels/dsepd/ss1978/lesson3/section3.html Case fatality rate Hospitalized cases Notification rate Notification rate in domestic cases Number of deaths case definition BFO:0000001 entity Entity Julius Caesar Verdi’s Requiem the Second World War your body mass index BFO 2 Reference: In all areas of empirical inquiry we encounter general terms of two sorts. First are general terms which refer to universals or types:animaltuberculosissurgical procedurediseaseSecond, are general terms used to refer to groups of entities which instantiate a given universal but do not correspond to the extension of any subuniversal of that universal because there is nothing intrinsic to the entities in question by virtue of which they – and only they – are counted as belonging to the given group. Examples are: animal purchased by the Emperortuberculosis diagnosed on a Wednesdaysurgical procedure performed on a patient from Stockholmperson identified as candidate for clinical trial #2056-555person who is signatory of Form 656-PPVpainting by Leonardo da VinciSuch terms, which represent what are called ‘specializations’ in [81 Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) entity Entity doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example Werner Ceusters 'portions of reality' include 4 sorts, entities (as BFO construes them), universals, configurations, and relations. It is an open question as to whether entities as construed in BFO will at some point also include these other portions of reality. See, for example, 'How to track absolutely everything' at http://www.referent-tracking.com/_RTU/papers/CeustersICbookRevised.pdf per discussion with Barry Smith An entity is anything that exists or has existed or will exist. (axiom label in BFO2 Reference: [001-001]) BFO:0000002 continuant Continuant An entity that exists in full at any time in which it exists at all, persists through time while maintaining its identity and has no temporal parts. BFO 2 Reference: Continuant entities are entities which can be sliced to yield parts only along the spatial dimension, yielding for example the parts of your table which we call its legs, its top, its nails. ‘My desk stretches from the window to the door. It has spatial parts, and can be sliced (in space) in two. With respect to time, however, a thing is a continuant.’ [60, p. 240 Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] continuant Continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. For example, in an expansion involving bringing in some of Ceuster's other portions of reality, questions are raised as to whether universals are continuants A continuant is an entity that persists, endures, or continues to exist through time while maintaining its identity. (axiom label in BFO2 Reference: [008-002]) if b is a continuant and if, for some t, c has_continuant_part b at t, then c is a continuant. (axiom label in BFO2 Reference: [126-001]) if b is a continuant and if, for some t, cis continuant_part of b at t, then c is a continuant. (axiom label in BFO2 Reference: [009-002]) if b is a material entity, then there is some temporal interval (referred to below as a one-dimensional temporal region) during which b exists. (axiom label in BFO2 Reference: [011-002]) (forall (x y) (if (and (Continuant x) (exists (t) (continuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [009-002] (forall (x y) (if (and (Continuant x) (exists (t) (hasContinuantPartOfAt y x t))) (Continuant y))) // axiom label in BFO2 CLIF: [126-001] (forall (x) (if (Continuant x) (Entity x))) // axiom label in BFO2 CLIF: [008-002] (forall (x) (if (Material Entity x) (exists (t) (and (TemporalRegion t) (existsAt x t))))) // axiom label in BFO2 CLIF: [011-002] BFO:0000003 occurrent Occurrent BFO 2 Reference: every occurrent that is not a temporal or spatiotemporal region is s-dependent on some independent continuant that is not a spatial region BFO 2 Reference: s-dependence obtains between every process and its participants in the sense that, as a matter of necessity, this process could not have existed unless these or those participants existed also. A process may have a succession of participants at different phases of its unfolding. Thus there may be different players on the field at different times during the course of a football game; but the process which is the entire game s-depends_on all of these players nonetheless. Some temporal parts of this process will s-depend_on on only some of the players. Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] occurrent Occurrent doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the sum of a process and the process boundary of another process. per discussion with Barry Smith Simons uses different terminology for relations of occurrents to regions: Denote the spatio-temporal location of a given occurrent e by 'spn[e]' and call this region its span. We may say an occurrent is at its span, in any larger region, and covers any smaller region. Now suppose we have fixed a frame of reference so that we can speak not merely of spatio-temporal but also of spatial regions (places) and temporal regions (times). The spread of an occurrent, (relative to a frame of reference) is the space it exactly occupies, and its spell is likewise the time it exactly occupies. We write 'spr[e]' and `spl[e]' respectively for the spread and spell of e, omitting mention of the frame. An occurrent is an entity that unfolds itself in time or it is the instantaneous boundary of such an entity (for example a beginning or an ending) or it is a temporal or spatiotemporal region which such an entity occupies_temporal_region or occupies_spatiotemporal_region. (axiom label in BFO2 Reference: [077-002]) Every occurrent occupies_spatiotemporal_region some spatiotemporal region. (axiom label in BFO2 Reference: [108-001]) b is an occurrent entity iff b is an entity that has temporal parts. (axiom label in BFO2 Reference: [079-001]) (forall (x) (if (Occurrent x) (exists (r) (and (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion x r))))) // axiom label in BFO2 CLIF: [108-001] (forall (x) (iff (Occurrent x) (and (Entity x) (exists (y) (temporalPartOf y x))))) // axiom label in BFO2 CLIF: [079-001] BFO:0000004 ic IndependentContinuant a chair a heart a leg a molecule a spatial region an atom an orchestra. an organism the bottom right portion of a human torso the interior of your mouth b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] independent continuant b is an independent continuant = Def. b is a continuant which is such that there is no c and no t such that b s-depends_on c at t. (axiom label in BFO2 Reference: [017-002]) For any independent continuant b and any time t there is some spatial region r such that b is located_in r at t. (axiom label in BFO2 Reference: [134-001]) For every independent continuant b and time t during the region of time spanned by its life, there are entities which s-depends_on b during t. (axiom label in BFO2 Reference: [018-002]) (forall (x t) (if (IndependentContinuant x) (exists (r) (and (SpatialRegion r) (locatedInAt x r t))))) // axiom label in BFO2 CLIF: [134-001] (forall (x t) (if (and (IndependentContinuant x) (existsAt x t)) (exists (y) (and (Entity y) (specificallyDependsOnAt y x t))))) // axiom label in BFO2 CLIF: [018-002] (iff (IndependentContinuant a) (and (Continuant a) (not (exists (b t) (specificallyDependsOnAt a b t))))) // axiom label in BFO2 CLIF: [017-002] BFO:0000006 s-region SpatialRegion BFO 2 Reference: Spatial regions do not participate in processes. Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] spatial region Spatial region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the union of a spatial point and a spatial line that doesn't overlap the point, or two spatial lines that intersect at a single point. In both cases the resultant spatial region is neither 0-dimensional, 1-dimensional, 2-dimensional, or 3-dimensional. per discussion with Barry Smith A spatial region is a continuant entity that is a continuant_part_of spaceR as defined relative to some frame R. (axiom label in BFO2 Reference: [035-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) All continuant parts of spatial regions are spatial regions. (axiom label in BFO2 Reference: [036-001]) (forall (x y t) (if (and (SpatialRegion x) (continuantPartOfAt y x t)) (SpatialRegion y))) // axiom label in BFO2 CLIF: [036-001] (forall (x) (if (SpatialRegion x) (Continuant x))) // axiom label in BFO2 CLIF: [035-001] BFO:0000008 t-region TemporalRegion Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] temporal region Temporal region doesn't have a closure axiom because the subclasses don't exhaust all possibilites. An example would be the mereological sum of a temporal instant and a temporal interval that doesn't overlap the instant. In this case the resultant temporal region is neither 0-dimensional nor 1-dimensional per discussion with Barry Smith A temporal region is an occurrent entity that is part of time as defined relative to some reference frame. (axiom label in BFO2 Reference: [100-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) All parts of temporal regions are temporal regions. (axiom label in BFO2 Reference: [101-001]) Every temporal region t is such that t occupies_temporal_region t. (axiom label in BFO2 Reference: [119-002]) (forall (r) (if (TemporalRegion r) (occupiesTemporalRegion r r))) // axiom label in BFO2 CLIF: [119-002] (forall (x y) (if (and (TemporalRegion x) (occurrentPartOf y x)) (TemporalRegion y))) // axiom label in BFO2 CLIF: [101-001] (forall (x) (if (TemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [100-001] BFO:0000009 2d-s-region TwoDimensionalSpatialRegion an infinitely thin plane in space. the surface of a sphere-shaped part of space A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] two-dimensional spatial region A two-dimensional spatial region is a spatial region that is of two dimensions. (axiom label in BFO2 Reference: [039-001]) (forall (x) (if (TwoDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [039-001] BFO:0000011 st-region SpatiotemporalRegion the spatiotemporal region occupied by a human life the spatiotemporal region occupied by a process of cellular meiosis. the spatiotemporal region occupied by the development of a cancer tumor A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region occupies_spatiotemporal_region itself. Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] spatiotemporal region A spatiotemporal region is an occurrent entity that is part of spacetime. (axiom label in BFO2 Reference: [095-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) All parts of spatiotemporal regions are spatiotemporal regions. (axiom label in BFO2 Reference: [096-001]) Each spatiotemporal region at any time t projects_onto some spatial region at t. (axiom label in BFO2 Reference: [099-001]) Each spatiotemporal region projects_onto some temporal region. (axiom label in BFO2 Reference: [098-001]) Every spatiotemporal region s is such that s occupies_spatiotemporal_region s. (axiom label in BFO2 Reference: [107-002]) (forall (r) (if (SpatioTemporalRegion r) (occupiesSpatioTemporalRegion r r))) // axiom label in BFO2 CLIF: [107-002] (forall (x t) (if (SpatioTemporalRegion x) (exists (y) (and (SpatialRegion y) (spatiallyProjectsOntoAt x y t))))) // axiom label in BFO2 CLIF: [099-001] (forall (x y) (if (and (SpatioTemporalRegion x) (occurrentPartOf y x)) (SpatioTemporalRegion y))) // axiom label in BFO2 CLIF: [096-001] (forall (x) (if (SpatioTemporalRegion x) (Occurrent x))) // axiom label in BFO2 CLIF: [095-001] (forall (x) (if (SpatioTemporalRegion x) (exists (y) (and (TemporalRegion y) (temporallyProjectsOnto x y))))) // axiom label in BFO2 CLIF: [098-001] BFO:0000015 process Process a process of cell-division, \ a beating of the heart a process of meiosis a process of sleeping the course of a disease the flight of a bird the life of an organism your process of aging. An occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) BFO 2 Reference: The realm of occurrents is less pervasively marked by the presence of natural units than is the case in the realm of independent continuants. Thus there is here no counterpart of ‘object’. In BFO 1.0 ‘process’ served as such a counterpart. In BFO 2.0 ‘process’ is, rather, the occurrent counterpart of ‘material entity’. Those natural – as contrasted with engineered, which here means: deliberately executed – units which do exist in the realm of occurrents are typically either parasitic on the existence of natural units on the continuant side, or they are fiat in nature. Thus we can count lives; we can count football games; we can count chemical reactions performed in experiments or in chemical manufacturing. We cannot count the processes taking place, for instance, in an episode of insect mating behavior.Even where natural units are identifiable, for example cycles in a cyclical process such as the beating of a heart or an organism’s sleep/wake cycle, the processes in question form a sequence with no discontinuities (temporal gaps) of the sort that we find for instance where billiard balls or zebrafish or planets are separated by clear spatial gaps. Lives of organisms are process units, but they too unfold in a continuous series from other, prior processes such as fertilization, and they unfold in turn in continuous series of post-life processes such as post-mortem decay. Clear examples of boundaries of processes are almost always of the fiat sort (midnight, a time of death as declared in an operating theater or on a death certificate, the initiation of a state of war) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] process p is a process = Def. p is an occurrent that has temporal proper parts and for some time t, p s-depends_on some material entity at t. (axiom label in BFO2 Reference: [083-003]) (iff (Process a) (and (Occurrent a) (exists (b) (properTemporalPartOf b a)) (exists (c t) (and (MaterialEntity c) (specificallyDependsOnAt a c t))))) // axiom label in BFO2 CLIF: [083-003] BFO:0000016 disposition Disposition an atom of element X has the disposition to decay to an atom of element Y certain people have a predisposition to colon cancer children are innately disposed to categorize objects in certain ways. the cell wall is disposed to filter chemicals in endocytosis and exocytosis BFO 2 Reference: Dispositions exist along a strength continuum. Weaker forms of disposition are realized in only a fraction of triggering cases. These forms occur in a significant number of cases of a similar type. b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] disposition b is a disposition means: b is a realizable entity & b’s bearer is some material entity & b is such that if it ceases to exist, then its bearer is physically changed, & b’s realization occurs when and because this bearer is in some special physical circumstances, & this realization occurs in virtue of the bearer’s physical make-up. (axiom label in BFO2 Reference: [062-002]) If b is a realizable entity then for all t at which b exists, b s-depends_on some material entity at t. (axiom label in BFO2 Reference: [063-002]) (forall (x t) (if (and (RealizableEntity x) (existsAt x t)) (exists (y) (and (MaterialEntity y) (specificallyDepends x y t))))) // axiom label in BFO2 CLIF: [063-002] (forall (x) (if (Disposition x) (and (RealizableEntity x) (exists (y) (and (MaterialEntity y) (bearerOfAt x y t)))))) // axiom label in BFO2 CLIF: [062-002] BFO:0000017 realizable RealizableEntity the disposition of this piece of metal to conduct electricity. the disposition of your blood to coagulate the function of your reproductive organs the role of being a doctor the role of this boundary to delineate where Utah and Colorado meet A specifically dependent continuant that inheres in continuant entities and are not exhibited in full at every time in which it inheres in an entity or group of entities. The exhibition or actualization of a realizable entity is a particular manifestation, functioning or process that occurs under certain circumstances. To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] realizable entity To say that b is a realizable entity is to say that b is a specifically dependent continuant that inheres in some independent continuant which is not a spatial region and is of a type instances of which are realized in processes of a correlated type. (axiom label in BFO2 Reference: [058-002]) All realizable dependent continuants have independent continuants that are not spatial regions as their bearers. (axiom label in BFO2 Reference: [060-002]) (forall (x t) (if (RealizableEntity x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (bearerOfAt y x t))))) // axiom label in BFO2 CLIF: [060-002] (forall (x) (if (RealizableEntity x) (and (SpecificallyDependentContinuant x) (exists (y) (and (IndependentContinuant y) (not (SpatialRegion y)) (inheresIn x y)))))) // axiom label in BFO2 CLIF: [058-002] BFO:0000018 0d-s-region ZeroDimensionalSpatialRegion A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] zero-dimensional spatial region A zero-dimensional spatial region is a point in space. (axiom label in BFO2 Reference: [037-001]) (forall (x) (if (ZeroDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [037-001] BFO:0000019 quality Quality the ambient temperature of this portion of air the color of a tomato the length of the circumference of your waist the mass of this piece of gold. the shape of your nose the shape of your nostril a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] quality a quality is a specifically dependent continuant that, in contrast to roles and dispositions, does not require any further process in order to be realized. (axiom label in BFO2 Reference: [055-001]) If an entity is a quality at any time that it exists, then it is a quality at every time that it exists. (axiom label in BFO2 Reference: [105-001]) (forall (x) (if (Quality x) (SpecificallyDependentContinuant x))) // axiom label in BFO2 CLIF: [055-001] (forall (x) (if (exists (t) (and (existsAt x t) (Quality x))) (forall (t_1) (if (existsAt x t_1) (Quality x))))) // axiom label in BFO2 CLIF: [105-001] BFO:0000020 sdc SpecificallyDependentContinuant Reciprocal specifically dependent continuants: the function of this key to open this lock and the mutually dependent disposition of this lock: to be opened by this key of one-sided specifically dependent continuants: the mass of this tomato of relational dependent continuants (multiple bearers): John’s love for Mary, the ownership relation between John and this statue, the relation of authority between John and his subordinates. the disposition of this fish to decay the function of this heart: to pump blood the mutual dependence of proton donors and acceptors in chemical reactions [79 the mutual dependence of the role predator and the role prey as played by two organisms in a given interaction the pink color of a medium rare piece of grilled filet mignon at its center the role of being a doctor the shape of this hole. the smell of this portion of mozzarella b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] specifically dependent continuant b is a specifically dependent continuant = Def. b is a continuant & there is some independent continuant c which is not a spatial region and which is such that b s-depends_on c at every time t during the course of b’s existence. (axiom label in BFO2 Reference: [050-003]) Specifically dependent continuant doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. We're not sure what else will develop here, but for example there are questions such as what are promises, obligation, etc. per discussion with Barry Smith (iff (SpecificallyDependentContinuant a) (and (Continuant a) (forall (t) (if (existsAt a t) (exists (b) (and (IndependentContinuant b) (not (SpatialRegion b)) (specificallyDependsOnAt a b t))))))) // axiom label in BFO2 CLIF: [050-003] BFO:0000023 role Role John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. the priest role the role of a boundary to demarcate two neighboring administrative territories the role of a building in serving as a military target the role of a stone in marking a property boundary the role of subject in a clinical trial the student role BFO 2 Reference: One major family of examples of non-rigid universals involves roles, and ontologies developed for corresponding administrative purposes may consist entirely of representatives of entities of this sort. Thus ‘professor’, defined as follows,b instance_of professor at t =Def. there is some c, c instance_of professor role & c inheres_in b at t.denotes a non-rigid universal and so also do ‘nurse’, ‘student’, ‘colonel’, ‘taxpayer’, and so forth. (These terms are all, in the jargon of philosophy, phase sortals.) By using role terms in definitions, we can create a BFO conformant treatment of such entities drawing on the fact that, while an instance of professor may be simultaneously an instance of trade union member, no instance of the type professor role is also (at any time) an instance of the type trade union member role (any more than any instance of the type color is at any time an instance of the type length).If an ontology of employment positions should be defined in terms of roles following the above pattern, this enables the ontology to do justice to the fact that individuals instantiate the corresponding universals – professor, sergeant, nurse – only during certain phases in their lives. b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] role b is a role means: b is a realizable entity & b exists because there is some single bearer that is in some special physical, social, or institutional set of circumstances in which this bearer does not have to be& b is not such that, if it ceases to exist, then the physical make-up of the bearer is thereby changed. (axiom label in BFO2 Reference: [061-001]) (forall (x) (if (Role x) (RealizableEntity x))) // axiom label in BFO2 CLIF: [061-001] BFO:0000024 fiat-object-part FiatObjectPart or with divisions drawn by cognitive subjects for practical reasons, such as the division of a cake (before slicing) into (what will become) slices (and thus member parts of an object aggregate). However, this does not mean that fiat object parts are dependent for their existence on divisions or delineations effected by cognitive subjects. If, for example, it is correct to conceive geological layers of the Earth as fiat object parts of the Earth, then even though these layers were first delineated in recent times, still existed long before such delineation and what holds of these layers (for example that the oldest layers are also the lowest layers) did not begin to hold because of our acts of delineation.Treatment of material entity in BFOExamples viewed by some as problematic cases for the trichotomy of fiat object part, object, and object aggregate include: a mussel on (and attached to) a rock, a slime mold, a pizza, a cloud, a galaxy, a railway train with engine and multiple carriages, a clonal stand of quaking aspen, a bacterial community (biofilm), a broken femur. Note that, as Aristotle already clearly recognized, such problematic cases – which lie at or near the penumbra of instances defined by the categories in question – need not invalidate these categories. The existence of grey objects does not prove that there are not objects which are black and objects which are white; the existence of mules does not prove that there are not objects which are donkeys and objects which are horses. It does, however, show that the examples in question need to be addressed carefully in order to show how they can be fitted into the proposed scheme, for example by recognizing additional subdivisions [29 the FMA:regional parts of an intact human body. the Western hemisphere of the Earth the division of the brain into regions the division of the planet into hemispheres the dorsal and ventral surfaces of the body the upper and lower lobes of the left lung BFO 2 Reference: Most examples of fiat object parts are associated with theoretically drawn divisions b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] fiat object part b is a fiat object part = Def. b is a material entity which is such that for all times t, if b exists at t then there is some object c such that b proper continuant_part of c at t and c is demarcated from the remainder of c by a two-dimensional continuant fiat boundary. (axiom label in BFO2 Reference: [027-004]) (forall (x) (if (FiatObjectPart x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y) (and (Object y) (properContinuantPartOfAt x y t)))))))) // axiom label in BFO2 CLIF: [027-004] BFO:0000026 1d-s-region OneDimensionalSpatialRegion an edge of a cube-shaped portion of space. A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] one-dimensional spatial region A one-dimensional spatial region is a line or aggregate of lines stretching from one point in space to another. (axiom label in BFO2 Reference: [038-001]) (forall (x) (if (OneDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [038-001] BFO:0000027 object-aggregate ObjectAggregate a collection of cells in a blood biobank. a swarm of bees is an aggregate of members who are linked together through natural bonds a symphony orchestra an organization is an aggregate whose member parts have roles of specific types (for example in a jazz band, a chess club, a football team) defined by fiat: the aggregate of members of an organization defined through physical attachment: the aggregate of atoms in a lump of granite defined through physical containment: the aggregate of molecules of carbon dioxide in a sealed container defined via attributive delimitations such as: the patients in this hospital the aggregate of bearings in a constant velocity axle joint the aggregate of blood cells in your body the nitrogen atoms in the atmosphere the restaurants in Palo Alto your collection of Meissen ceramic plates. An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects BFO 2 Reference: object aggregates may gain and lose parts while remaining numerically identical (one and the same individual) over time. This holds both for aggregates whose membership is determined naturally (the aggregate of cells in your body) and aggregates determined by fiat (a baseball team, a congressional committee). ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] object aggregate An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects An entity a is an object aggregate if and only if there is a mutually exhaustive and pairwise disjoint partition of a into objects ISBN:978-3-938793-98-5pp124-158#Thomas Bittner and Barry Smith, 'A Theory of Granular Partitions', in K. Munn and B. Smith (eds.), Applied Ontology: An Introduction, Frankfurt/Lancaster: ontos, 2008, 125-158. b is an object aggregate means: b is a material entity consisting exactly of a plurality of objects as member_parts at all times at which b exists. (axiom label in BFO2 Reference: [025-004]) (forall (x) (if (ObjectAggregate x) (and (MaterialEntity x) (forall (t) (if (existsAt x t) (exists (y z) (and (Object y) (Object z) (memberPartOfAt y x t) (memberPartOfAt z x t) (not (= y z)))))) (not (exists (w t_1) (and (memberPartOfAt w x t_1) (not (Object w)))))))) // axiom label in BFO2 CLIF: [025-004] BFO:0000028 3d-s-region ThreeDimensionalSpatialRegion a cube-shaped region of space a sphere-shaped region of space, A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] three-dimensional spatial region A three-dimensional spatial region is a spatial region that is of three dimensions. (axiom label in BFO2 Reference: [040-001]) (forall (x) (if (ThreeDimensionalSpatialRegion x) (SpatialRegion x))) // axiom label in BFO2 CLIF: [040-001] BFO:0000029 site Site Manhattan Canyon) a hole in the interior of a portion of cheese a rabbit hole an air traffic control region defined in the airspace above an airport the Grand Canyon the Piazza San Marco the cockpit of an aircraft the hold of a ship the interior of a kangaroo pouch the interior of the trunk of your car the interior of your bedroom the interior of your office the interior of your refrigerator the lumen of your gut your left nostril (a fiat part – the opening – of your left nasal cavity) b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] Note that this can refer to a material entity like an organ or muscle, or an immaterial entity (a site or fiat boundary) like skin, stomach cavity or lung surface. site b is a site means: b is a three-dimensional immaterial entity that is (partially or wholly) bounded by a material entity or it is a three-dimensional immaterial part thereof. (axiom label in BFO2 Reference: [034-002]) (forall (x) (if (Site x) (ImmaterialEntity x))) // axiom label in BFO2 CLIF: [034-002] BFO:0000030 object Object atom cell cells and organisms engineered artifacts grain of sand molecule organelle organism planet solid portions of matter star BFO 2 Reference: BFO rests on the presupposition that at multiple micro-, meso- and macroscopic scales reality exhibits certain stable, spatially separated or separable material units, combined or combinable into aggregates of various sorts (for example organisms into what are called ‘populations’). Such units play a central role in almost all domains of natural science from particle physics to cosmology. Many scientific laws govern the units in question, employing general terms (such as ‘molecule’ or ‘planet’) referring to the types and subtypes of units, and also to the types and subtypes of the processes through which such units develop and interact. The division of reality into such natural units is at the heart of biological science, as also is the fact that these units may form higher-level units (as cells form multicellular organisms) and that they may also form aggregates of units, for example as cells form portions of tissue and organs form families, herds, breeds, species, and so on. At the same time, the division of certain portions of reality into engineered units (manufactured artifacts) is the basis of modern industrial technology, which rests on the distributed mass production of engineered parts through division of labor and on their assembly into larger, compound units such as cars and laptops. The division of portions of reality into units is one starting point for the phenomenon of counting. BFO 2 Reference: Each object is such that there are entities of which we can assert unproblematically that they lie in its interior, and other entities of which we can assert unproblematically that they lie in its exterior. This may not be so for entities lying at or near the boundary between the interior and exterior. This means that two objects – for example the two cells depicted in Figure 3 – may be such that there are material entities crossing their boundaries which belong determinately to neither cell. Something similar obtains in certain cases of conjoined twins (see below). BFO 2 Reference: To say that b is causally unified means: b is a material entity which is such that its material parts are tied together in such a way that, in environments typical for entities of the type in question,if c, a continuant part of b that is in the interior of b at t, is larger than a certain threshold size (which will be determined differently from case to case, depending on factors such as porosity of external cover) and is moved in space to be at t at a location on the exterior of the spatial region that had been occupied by b at t, then either b’s other parts will be moved in coordinated fashion or b will be damaged (be affected, for example, by breakage or tearing) in the interval between t and t.causal changes in one part of b can have consequences for other parts of b without the mediation of any entity that lies on the exterior of b. Material entities with no proper material parts would satisfy these conditions trivially. Candidate examples of types of causal unity for material entities of more complex sorts are as follows (this is not intended to be an exhaustive list):CU1: Causal unity via physical coveringHere the parts in the interior of the unified entity are combined together causally through a common membrane or other physical covering\. The latter points outwards toward and may serve a protective function in relation to what lies on the exterior of the entity [13, 47 BFO 2 Reference: an object is a maximal causally unified material entity BFO 2 Reference: ‘objects’ are sometimes referred to as ‘grains’ [74 b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) object b is an object means: b is a material entity which manifests causal unity of one or other of the types CUn listed above & is of a type (a material universal) instances of which are maximal relative to this criterion of causal unity. (axiom label in BFO2 Reference: [024-001]) BFO:0000031 gdc GenericallyDependentContinuant The entries in your database are patterns instantiated as quality instances in your hard drive. The database itself is an aggregate of such patterns. When you create the database you create a particular instance of the generically dependent continuant type database. Each entry in the database is an instance of the generically dependent continuant type IAO: information content entity. the pdf file on your laptop, the pdf file that is a copy thereof on my laptop the sequence of this protein molecule; the sequence that is a copy thereof in that protein molecule. A continuant that is dependent on one or other independent continuant bearers. For every instance of A requires some instance of (an independent continuant type) B but which instance of B serves can change from time to time. b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] generically dependent continuant b is a generically dependent continuant = Def. b is a continuant that g-depends_on one or more other entities. (axiom label in BFO2 Reference: [074-001]) (iff (GenericallyDependentContinuant a) (and (Continuant a) (exists (b t) (genericallyDependsOnAt a b t)))) // axiom label in BFO2 CLIF: [074-001] BFO:0000034 function Function the function of a hammer to drive in nails the function of a heart pacemaker to regulate the beating of a heart through electricity the function of amylase in saliva to break down starch into sugar BFO 2 Reference: In the past, we have distinguished two varieties of function, artifactual function and biological function. These are not asserted subtypes of BFO:function however, since the same function – for example: to pump, to transport – can exist both in artifacts and in biological entities. The asserted subtypes of function that would be needed in order to yield a separate monoheirarchy are not artifactual function, biological function, etc., but rather transporting function, pumping function, etc. A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] function A function is a disposition that exists in virtue of the bearer’s physical make-up and this physical make-up is something the bearer possesses because it came into being, either through evolution (in the case of natural biological entities) or through intentional design (in the case of artifacts), in order to realize processes of a certain sort. (axiom label in BFO2 Reference: [064-001]) (forall (x) (if (Function x) (Disposition x))) // axiom label in BFO2 CLIF: [064-001] BFO:0000035 p-boundary ProcessBoundary the boundary between the 2nd and 3rd year of your life. p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] process boundary p is a process boundary =Def. p is a temporal part of a process & p has no proper temporal parts. (axiom label in BFO2 Reference: [084-001]) Every process boundary occupies_temporal_region a zero-dimensional temporal region. (axiom label in BFO2 Reference: [085-002]) (forall (x) (if (ProcessBoundary x) (exists (y) (and (ZeroDimensionalTemporalRegion y) (occupiesTemporalRegion x y))))) // axiom label in BFO2 CLIF: [085-002] (iff (ProcessBoundary a) (exists (p) (and (Process p) (temporalPartOf a p) (not (exists (b) (properTemporalPartOf b a)))))) // axiom label in BFO2 CLIF: [084-001] BFO:0000038 1d-t-region OneDimensionalTemporalRegion the temporal region during which a process occurs. BFO 2 Reference: A temporal interval is a special kind of one-dimensional temporal region, namely one that is self-connected (is without gaps or breaks). A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] one-dimensional temporal region A one-dimensional temporal region is a temporal region that is extended. (axiom label in BFO2 Reference: [103-001]) (forall (x) (if (OneDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [103-001] BFO:0000040 material MaterialEntity a flame a forest fire a human being a hurricane a photon a puff of smoke a sea wave a tornado an aggregate of human beings. an energy wave an epidemic the undetached arm of a human being BFO 2 Reference: Material entities (continuants) can preserve their identity even while gaining and losing material parts. Continuants are contrasted with occurrents, which unfold themselves in successive temporal parts or phases [60 BFO 2 Reference: Object, Fiat Object Part and Object Aggregate are not intended to be exhaustive of Material Entity. Users are invited to propose new subcategories of Material Entity. BFO 2 Reference: ‘Matter’ is intended to encompass both mass and energy (we will address the ontological treatment of portions of energy in a later version of BFO). A portion of matter is anything that includes elementary particles among its proper or improper parts: quarks and leptons, including electrons, as the smallest particles thus far discovered; baryons (including protons and neutrons) at a higher level of granularity; atoms and molecules at still higher levels, forming the cells, organs, organisms and other material entities studied by biologists, the portions of rock studied by geologists, the fossils studied by paleontologists, and so on.Material entities are three-dimensional entities (entities extended in three spatial dimensions), as contrasted with the processes in which they participate, which are four-dimensional entities (entities extended also along the dimension of time).According to the FMA, material entities may have immaterial entities as parts – including the entities identified below as sites; for example the interior (or ‘lumen’) of your small intestine is a part of your body. BFO 2.0 embodies a decision to follow the FMA here. A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] material entity A material entity is an independent continuant that has some portion of matter as proper or improper continuant part. (axiom label in BFO2 Reference: [019-002]) Every entity which has a material entity as continuant part is a material entity. (axiom label in BFO2 Reference: [020-002]) every entity of which a material entity is continuant part is also a material entity. (axiom label in BFO2 Reference: [021-002]) (forall (x) (if (MaterialEntity x) (IndependentContinuant x))) // axiom label in BFO2 CLIF: [019-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt x y t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [021-002] (forall (x) (if (and (Entity x) (exists (y t) (and (MaterialEntity y) (continuantPartOfAt y x t)))) (MaterialEntity x))) // axiom label in BFO2 CLIF: [020-002] BFO:0000140 cf-boundary ContinuantFiatBoundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) BFO 2 Reference: In BFO 1.1 the assumption was made that the external surface of a material entity such as a cell could be treated as if it were a boundary in the mathematical sense. The new document propounds the view that when we talk about external surfaces of material objects in this way then we are talking about something fiat. To be dealt with in a future version: fiat boundaries at different levels of granularity.More generally, the focus in discussion of boundaries in BFO 2.0 is now on fiat boundaries, which means: boundaries for which there is no assumption that they coincide with physical discontinuities. The ontology of boundaries becomes more closely allied with the ontology of regions. BFO 2 Reference: a continuant fiat boundary is a boundary of some material entity (for example: the plane separating the Northern and Southern hemispheres; the North Pole), or it is a boundary of some immaterial entity (for example of some portion of airspace). Three basic kinds of continuant fiat boundary can be distinguished (together with various combination kinds [29 Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. Every continuant fiat boundary is located at some spatial region at every time at which it exists (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] continuant fiat boundary b is a continuant fiat boundary = Def. b is an immaterial entity that is of zero, one or two dimensions and does not include a spatial region as part. (axiom label in BFO2 Reference: [029-001]) Continuant fiat boundary doesn't have a closure axiom because the subclasses don't necessarily exhaust all possibilites. An example would be the mereological sum of two-dimensional continuant fiat boundary and a one dimensional continuant fiat boundary that doesn't overlap it. The situation is analogous to temporal and spatial regions. (iff (ContinuantFiatBoundary a) (and (ImmaterialEntity a) (exists (b) (and (or (ZeroDimensionalSpatialRegion b) (OneDimensionalSpatialRegion b) (TwoDimensionalSpatialRegion b)) (forall (t) (locatedInAt a b t)))) (not (exists (c t) (and (SpatialRegion c) (continuantPartOfAt c a t)))))) // axiom label in BFO2 CLIF: [029-001] BFO:0000141 immaterial ImmaterialEntity BFO 2 Reference: Immaterial entities are divided into two subgroups:boundaries and sites, which bound, or are demarcated in relation, to material entities, and which can thus change location, shape and size and as their material hosts move or change shape or size (for example: your nasal passage; the hold of a ship; the boundary of Wales (which moves with the rotation of the Earth) [38, 7, 10 immaterial entity BFO:0000142 1d-cf-boundary OneDimensionalContinuantFiatBoundary The Equator all geopolitical boundaries all lines of latitude and longitude the line separating the outer surface of the mucosa of the lower lip from the outer surface of the skin of the chin. the median sulcus of your tongue a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] one-dimensional continuant fiat boundary a one-dimensional continuant fiat boundary is a continuous fiat line whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [032-001]) (iff (OneDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (OneDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [032-001] BFO:0000144 process-profile ProcessProfile On a somewhat higher level of complexity are what we shall call rate process profiles, which are the targets of selective abstraction focused not on determinate quality magnitudes plotted over time, but rather on certain ratios between these magnitudes and elapsed times. A speed process profile, for example, is represented by a graph plotting against time the ratio of distance covered per unit of time. Since rates may change, and since such changes, too, may have rates of change, we have to deal here with a hierarchy of process profile universals at successive levels One important sub-family of rate process profiles is illustrated by the beat or frequency profiles of cyclical processes, illustrated by the 60 beats per minute beating process of John’s heart, or the 120 beats per minute drumming process involved in one of John’s performances in a rock band, and so on. Each such process includes what we shall call a beat process profile instance as part, a subtype of rate process profile in which the salient ratio is not distance covered but rather number of beat cycles per unit of time. Each beat process profile instance instantiates the determinable universal beat process profile. But it also instantiates multiple more specialized universals at lower levels of generality, selected from rate process profilebeat process profileregular beat process profile3 bpm beat process profile4 bpm beat process profileirregular beat process profileincreasing beat process profileand so on.In the case of a regular beat process profile, a rate can be assigned in the simplest possible fashion by dividing the number of cycles by the length of the temporal region occupied by the beating process profile as a whole. Irregular process profiles of this sort, for example as identified in the clinic, or in the readings on an aircraft instrument panel, are often of diagnostic significance. The simplest type of process profiles are what we shall call ‘quality process profiles’, which are the process profiles which serve as the foci of the sort of selective abstraction that is involved when measurements are made of changes in single qualities, as illustrated, for example, by process profiles of mass, temperature, aortic pressure, and so on. b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] process profile b is a process_profile =Def. there is some process c such that b process_profile_of c (axiom label in BFO2 Reference: [093-002]) b process_profile_of c holds when b proper_occurrent_part_of c& there is some proper_occurrent_part d of c which has no parts in common with b & is mutually dependent on b& is such that b, c and d occupy the same temporal region (axiom label in BFO2 Reference: [094-005]) (forall (x y) (if (processProfileOf x y) (and (properContinuantPartOf x y) (exists (z t) (and (properOccurrentPartOf z y) (TemporalRegion t) (occupiesSpatioTemporalRegion x t) (occupiesSpatioTemporalRegion y t) (occupiesSpatioTemporalRegion z t) (not (exists (w) (and (occurrentPartOf w x) (occurrentPartOf w z))))))))) // axiom label in BFO2 CLIF: [094-005] (iff (ProcessProfile a) (exists (b) (and (Process b) (processProfileOf a b)))) // axiom label in BFO2 CLIF: [093-002] BFO:0000145 r-quality RelationalQuality John’s role of husband to Mary is dependent on Mary’s role of wife to John, and both are dependent on the object aggregate comprising John and Mary as member parts joined together through the relational quality of being married. a marriage bond, an instance of love, an obligation between one person and another. b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] relational quality b is a relational quality = Def. for some independent continuants c, d and for some time t: b quality_of c at t & b quality_of d at t. (axiom label in BFO2 Reference: [057-001]) (iff (RelationalQuality a) (exists (b c t) (and (IndependentContinuant b) (IndependentContinuant c) (qualityOfAt a b t) (qualityOfAt a c t)))) // axiom label in BFO2 CLIF: [057-001] BFO:0000146 2d-cf-boundary TwoDimensionalContinuantFiatBoundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] two-dimensional continuant fiat boundary a two-dimensional continuant fiat boundary (surface) is a self-connected fiat surface whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [033-001]) (iff (TwoDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (TwoDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [033-001] BFO:0000147 0d-cf-boundary ZeroDimensionalContinuantFiatBoundary the geographic North Pole the point of origin of some spatial coordinate system. the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] zero-dimensional continuant fiat boundary zero dimension continuant fiat boundaries are not spatial points. Considering the example 'the quadripoint where the boundaries of Colorado, Utah, New Mexico, and Arizona meet' : There are many frames in which that point is zooming through many points in space. Whereas, no matter what the frame, the quadripoint is always in the same relation to the boundaries of Colorado, Utah, New Mexico, and Arizona. requested by Melanie Courtot a zero-dimensional continuant fiat boundary is a fiat point whose location is defined in relation to some material entity. (axiom label in BFO2 Reference: [031-001]) (iff (ZeroDimensionalContinuantFiatBoundary a) (and (ContinuantFiatBoundary a) (exists (b) (and (ZeroDimensionalSpatialRegion b) (forall (t) (locatedInAt a b t)))))) // axiom label in BFO2 CLIF: [031-001] BFO:0000148 0d-t-region ZeroDimensionalTemporalRegion a temporal region that is occupied by a process boundary right now the moment at which a child is born the moment at which a finger is detached in an industrial accident the moment of death. temporal instant. A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] zero-dimensional temporal region A zero-dimensional temporal region is a temporal region that is without extent. (axiom label in BFO2 Reference: [102-001]) (forall (x) (if (ZeroDimensionalTemporalRegion x) (TemporalRegion x))) // axiom label in BFO2 CLIF: [102-001] BFO:0000182 history History A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) history A history is a process that is the sum of the totality of processes taking place in the spatiotemporal region occupied by a material entity or site, including processes on the surface of the entity or within the cavities to which it serves as host. (axiom label in BFO2 Reference: [138-001]) CHMO:0000993 An independent material continuant that is self-connected and retains its identity over time. portion of material CHMO:0002743 specimen extraction matrix Those components of a sample that are not measured by an experiment. "This observable is important where process of capturing sample can affect dna extraction." matrix A bacterial infectious disease that results_in infection by bacteria as a result of their presence or activity within the normal, healthy host, and their intrinsic virulence is, in part, a necessary consequence of their need to reproduce and spread. disease_ontology DOID:0050338 primary bacterial infectious disease DOID:0050338 A bacterial infectious disease that results_in infection by bacteria as a result of their presence or activity within the normal, healthy host, and their intrinsic virulence is, in part, a necessary consequence of their need to reproduce and spread. url:http://en.wikipedia.org/wiki/Infectious_disease A primary bacterial infectious disease caused by the bacteria of the genus Salmonella. It has sypmtoms diarrhea, fever, vomiting, and abdominal cramps 12 to 72 hours after infection. In most cases, the illness lasts four to seven days, and most people recover without treatment. ICD10CM:A02.0 ICD9CM:003.0 Salmonella infection disease_ontology DOID:0060859 salmonellosis DOID:0060859 A primary bacterial infectious disease caused by the bacteria of the genus Salmonella. It has sypmtoms diarrhea, fever, vomiting, and abdominal cramps 12 to 72 hours after infection. In most cases, the illness lasts four to seven days, and most people recover without treatment. url:https://www.cdc.gov/salmonella/general/index.html url:https://www.foodsafety.gov/poisoning/causes/bacteriaviruses/salmonella A disease by infectious agent that results_in infection, has_material_basis_in Bacteria. ICD10CM:A49.9 MESH:D001424 NCI:C2890 SNOMEDCT_US_2020_03_01:87628006 UMLS_CUI:C0004623 disease_ontology DOID:104 bacterial infectious disease DOID:104 A disease by infectious agent that results_in infection, has_material_basis_in Bacteria. url:http://en.wikipedia.org/wiki/Pathogenic_bacteria A primary bacterial infectious disease that results_in infection located_in intestine, has_material_basis_in Campylobacter jejuni, which is transmitted_by ingestion of contaminated food or water or transmitted_by contact with infected people or animals. The infection has_symptom diarrhea or has_symptom dysentery, has_symptom abdominal cramps and pain, and has_symptom fever. DOID:13621 MESH:D002169 SNOMEDCT_US_2020_03_01:86500004 UMLS_CUI:C0006818 Campylobacteriosis disease_ontology DOID:13622 campylobacteriosis DOID:13622 A primary bacterial infectious disease that results_in infection located_in intestine, has_material_basis_in Campylobacter jejuni, which is transmitted_by ingestion of contaminated food or water or transmitted_by contact with infected people or animals. The infection has_symptom diarrhea or has_symptom dysentery, has_symptom abdominal cramps and pain, and has_symptom fever. url:http://en.wikipedia.org/wiki/Campylobacteriosis url:http://www.health.state.ny.us/diseases/communicable/campylobacteriosis/fact_sheet.htm A gastrointestinal system infectious disease that involves inflammation of the lining of the stomach and small and large intestines, which is caused by viruses, bacteria, or parasites. Chemicals and drugs also cause gastroenteritis. The symptoms include diarrhea, loss of appetite, nausea, vomiting, cramps, and discomfort in the abdomen. DOID:4094 DOID:5269 ICD10CM:K52.9 MESH:D005759 NCI:C34632 SNOMEDCT_US_2020_03_01:154278002 UMLS_CUI:C0017160 cholera morbus infectious colitis, enteritis and gastroenteritis disease_ontology DOID:2326 gastroenteritis MESH:D005759 DOID:2326 A gastrointestinal system infectious disease that involves inflammation of the lining of the stomach and small and large intestines, which is caused by viruses, bacteria, or parasites. Chemicals and drugs also cause gastroenteritis. The symptoms include diarrhea, loss of appetite, nausea, vomiting, cramps, and discomfort in the abdomen. url:http://www.merck.com/mmhe/sec09/ch122/ch122a.html A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. MESH:D004194 NCI:C2991 SNOMEDCT_US_2020_03_01:64572001 UMLS_CUI:C0012634 disease_ontology DOID:4 disease DOID:4 A disease is a disposition (i) to undergo pathological processes that (ii) exists in an organism because of one or more disorders in that organism. url:http://ontology.buffalo.edu/medo/Disease_and_Diagnosis.pdf A disease that manifests in a defined anatomical structure. DOID:1 DOID:2 DOID:5 DOID:71 DOID:72 DOID:8 disease_ontology DOID:7 disease of anatomical entity DOID:7 A disease that manifests in a defined anatomical structure. url:http://www2.merriam-webster.com/cgi-bin/mwmednlm?book=Medical&va=anatomic A disease of anatomical entity that is located_in the gastrointestinal tract. DOID:27 DOID:944 ICD10CM:K92.9 ICD9CM:520-579.99 MESH:D004066 SNOMEDCT_US_2020_03_01:53619000 UMLS_CUI:C0012242 GIT disease Gastroenteropathy alimentary system disease digestive system disorder gastrointestinal disease gastrointestinal disorder disease_ontology DOID:77 gastrointestinal system disease DOID:77 A disease of anatomical entity that is located_in the gastrointestinal tract. url:http://en.wikipedia.org/wiki/Human_gastrointestinal_tract ENVO:00000004 FTT:1242 FTT:1252 FTT:15 FTT:16 FTT:18 FTT:19 FTT:21 FTT:22 FTT:23 FTT:24 FTT:25 FTT:26 FTT:27 FTT:28 FTT:29 FTT:37 SWEETRealm:AdministrativeRegion TGN:80001 TGN:81099 TGN:81123 https://en.wikipedia.org/wiki/Administrative_region administrative area administrative region ENVO:00000005 state / province / territory / region lookup:http://purl.obolibrary.org/obo/GAZ_00000448 A primary administrative division of a country, such as a state in the United States. A primary administrative division of a country, such as a state in the United States. FTT:414 FTT:569 Geonames:A.ADM1 TGN:81100 first-order administrative region first-order administrative region ENVO:00000009 A political association with effective dominion over a geographic area. FTT:424 FTT:566 FTT:567 FTT:571 SWEETRealm:Country SWEETRealm:State TGN:80006 TGN:81010 TGN:81011 TGN:81102 https://en.wikipedia.org/wiki/Nation http://purl.obolibrary.org/obo/NCIT_C25464 nation independent nation independent political entity independent sovereign nation national geopolitical entity ENVO:00000062 Place or area with clustered or scattered buildings and a permanent human population. place FTT:1097 FTT:33 Geonames:P.PPL Geonames:P.PPLS TGN:22201 TGN:83002 https://en.wikipedia.org/wiki/Populated_place inhabited place populated place populated places settlement populated place ENVO:00000123 A geographical region whose affairs and population are administered by an authority. FTT:1093 Geonames:A.PCL TGN:80002 political entity ENVO:00000856 Incorporated populated place. urban area EcoLexicon:city FTT:430 FTT:483 FTT:484 FTT:485 SWEETRealm:City TGN:83020 TGN:83040 TGN:83043 https://en.wikipedia.org/wiki/City http://purl.obolibrary.org/obo/NCIT_C80234 city ENVO:01000408 A site which has its extent determined by the presence or influence of one or more components of an environmental system or the processes occurring therein. An environmental zone is an environmental feature whose extent is determined by the presence or influence of one or more material entities or processes. An environmental zone may, itself, assume the role of an environmental feature. envoPolar For example, a intertidal zone is that part of a coast which is exposed to air and water due to tidal processes. It determines the intertidal zone environment. This class is experimental and not suitable for annotation! "Zone" is likely to become some form of BFO:site. It is intended to capture entities from both physiography and human geography. Formerly, this class was an experimental class and a subclass of "environmental feature". It is now aligned to BFO. The class was not obsoleted as the core semantics maintained their stability through its transition. environmental zone ENVO:01000658 A settlement with a high density of buildings and inhabitants. The thresholds for what makes a settlment "dense" can be determined as needed. If there is a specific threshold that should be added to ENVO, please make a new class request. dense settlement GAZ:00000448 A reference to a place on the Earth, by its name or by its geographical location. GAZ:00000467 geographic region {alternative name} geographic location GENEPIO:0001742 region lookup:http://purl.obolibrary.org/obo/GAZ_00000448 A subnational region is a type of subnational entity similar to a nation's state, province, or territory. Damion Dooley subnational region GENEPIO:0001790 This is a catch-all category for listing specimen related terms Damion Dooley specimen datum http://purl.obolibrary.org/obo/GENEPIO_0002105 http://purl.obolibrary.org/obo/OBI_0001616 GENEPIO:0001886 A designated area on earth is one or more areas defined by one or more boundaries. A boundary can be defined by a polygon perimeter, a lat/long and radius, or a fiat-boundary geographic featureset like a named river channel or mountain ridge; it may have one or more names associated with it. Note that areas associated with a name may change their boundary definitions over time. Damion Dooley designated area on Earth HSO:0000001 a planned process which systematically, continuously or repeatedly measures, collected, collates, analyses, interprets and disseminates health and welfare related data from defined populations. A specific surveillance activity that is planned and has (or will have) associated results. A surveillance component or a surveillance system could both be a surveillance activity. Ideally, every activity would have unique attributes for methods - for instance, only one sampling stage. If samples are collected in a slaughterhouse AND in farms, these would ideally be modeled as two different activities, and the appropriate properties used to declare them as linked. But since activities are not defined the same in every health surveillance sector, nor do all data support such a granularity, the class is able to model methods and results for any surveillance activity declared. One surveillance activity should have an unique identifier, to which results are linked. The act of being a "planned activity" is used in the context of OBI, where his implies the existence of a protocol for action. Therefore, surveillance activities such as outbreak investigations, are also considered a planned process (even if the outbreak itself is not a planned occurrence, the response to one is planned for). Surveillance Activity HSO:0000014 a role given to a specific herd of domesticated animals, specifying that they are raised in an agricultural setting with a specific purpose. livestock farming system HSO:0000015 Classification of livstock farming systems based on the type of commodity produced. Sub-classes are not mutually exclusive. product oriented farming type HSO:0000016 MTX A0C7P Animals farmed for egg production purposes egg production HSO:0000017 MTX A0C7G Animals farmed for meat production purposes meat production HSO:0000018 MTX A0C7N Animals farmed for milk production purposes milk production milk production HSO:0000019 MTX A0C7G Animals farmed for breeding purposes reproducer HSO:0000057 supra-national geopolitical entity HSO:0000058 NUTS region HSO:0000059 language HSO:0000060 A directive information that qualifies/classifies specimens. Can be inferred if enough information about the specimen is given, but can also be assigned directly when the source of information only specifies the type of speciment (for instance when using the SSD2 terminology, catalog MTXTYP). matrix type HSO:0000061 whole organism HSO:0000062 a specimen collected from an organism. inferred categorization of specimens based on the informaiton provided in matrix type and/or regarding the anatomical entity targetted matrix from organism HSO:0000063 fluid specimen HSO:0000064 organ/tissue specimen HSO:0000065 swab specimen HSO:0000066 excreta specimen HSO:0000070 A directive information that describes the context for data collection in support to a specificsurveillance objective. https://github.com/SVA-SE/AHSURED/wiki surveillance context HSO:0000071 A directive information used to describe the type of agent who carries out the data collection in a surveillance activity surveillance sampler type SAMPLR surveillance executor type SAMPLR HSO:0000072 A directive information that describes how population units will be chosen for sample/data collection in a surveillance activity. https://github.com/SVA-SE/AHSURED/wiki/Description-of-surveillance-items-in-the-checklist https://www.fp7-risksur.eu/terminology/glossary Describe how units have been planned to be sampled Sampling at the primary sampling unit (PSU) level Describe the information used to calculate sample size at the PSU level, e.g. the number of PSU in the population (see section 6 also), (between−herd) design prevalence, desired confidence, desired power, sensitivity, specificity. If recommended parameters from international standards are used, indicate the source of such standards (e.g. OIE) Sampling at the secondary sampling unit (SSU) level Describe the information used to calculate sample size at the SSU level, e.g. the number of SSU in the population (see section 6 also), (within−herd) design prevalence, desired confidence, desired power, sensitivity, specificity. sampling strategy HSO:0000073 A sampling unit is one of the units into which an aggregate is divided for the purpose of sampling, each unit being regarded as individual and indivisible when the selection is made. https://stats.oecd.org/glossary/index.htm sampling unit HSO:0000201 Information about an assay which can be used to find of qualify/classify assays. assay datum HSO:0000202 Known diagnostic tests can be classified into groups here so that information such as whether they are an antibody detection or pathogen identification information can be associated to the test, even if this information is not detailed in the data source. As an example, diagnostic tests classifications contained in existing terminologies (such as EFSA SSD2, https://www.efsa.europa.eu/en/efsajournal/pub/3424) can be used to create specific test catehories here. A test category used to group diagnostic tests based on generla characteristics, such as the target for detection (antigen or antibody). Categorization of diagnostic tests used in health surveillance. This information can be assigned to a test, or inferred from test characteristics if enough information is given about it. diagnostic test type HSO:0000245 fecal swab versus a fecal specimen will both have anatomical entity feces, but one will be a swab specimen and the other will be a excreta specimen. A specimen datum used, in conjunction with information about the target sampled anatomical location, in order to specify _how_ the anatomical entity was sampled specimen from organism type HSO:0000246 whole organism specimen HSO:0000247 fluid specimen HSO:0000248 organ/tissue specimen HSO:0000249 excreta specimen HSO:0000250 swab specimen HSO:0000252 s specimen categorization which described the type of entity from which the specimen was collected inferred categorization of specimens based on the matrix type informaiton provided regarding their source specimen by origin HSO:0000253 animal specimen HSO:0000254 food specimen HSO:0000255 environmental specimen HSO:0000256 A collection of all directive information associated with a surveillance activity, such as the surveillance objectives, the action specifications and legislative specification. Everything about a surveillance activity that is related to its planning and methodology. A surveillance activity is then a specific execution of a surveillance protocol, which generates specific results. A surveillance protocol exists efore a surveillance activity is carried out, and can exist even in the absence of a surveillance activity - for instance there cna be a surveillance protocol for outbreak investigations, but the exucition of a surveillance activity and associated results will only be available if an outbreak is detected. surveillance protocol HSO:0000261 A directive information that details the legislative body that supports a specific surveillance activity, or the specific obligations prescried in these legislation. All the laws or regulations of a country or region which are related to the obligations or permissions associated with a specific surveillance activity. legislative specification HSO:0000264 A directive information that described those goal(s) that when met will result in the collection and analysis of data in order to achieve the purpose of the system OIE (2014a). Guide to terrestrial animal health surveillance. Paris, France, OIE. https://www.fp7-risksur.eu/terminology/glossary surveillance objective HSO:0000265 A directive information that describes why surveillance is necessary and what it will accomplish. https://github.com/SVA-SE/AHSURED/wiki/ https://www.fp7-risksur.eu/terminology/glossary surveillance purpose HSO:0000268 A surveillance objective to search for any animals affected, clinically or not, by the hazard under surveillance. https://github.com/SVA-SE/AHSURED/wiki This objective is appropriate if the hazard is present, regardless of whether the hazard occurrence is endemic, epidemic or sporadic, and action will be taken to control disease whenever it is detected. case detection HSO:0000269 A surveillance objective to gather evidence that can demonstrate, with a given confidence level, that a specific hazard is not present in a given population. https://github.com/SVA-SE/AHSURED/wiki This objective is appropriate if the target hazard is thought to be absent in the territory to be covered and the aim is to demonstrate disease freedom for trade or non−trade purposes (e.g. improve public health, to decide when to stop an eradication programme and to eliminate production losses and control costs due to endemic disease). This may apply to diseases which a) have been historically absent, b) have been eradicated and official freedom has been confirmed or c) are thought to be eradicated, but official freedom has not yet been confirmed. demonstration of disease freedom HSO:0000270 A surveillance objective to detect any hazard cases as soon as possible. https://github.com/SVA-SE/AHSURED/wiki This objective is appropriate for a situation where the disease is currently absent in the country or region. It may be applied to surveillance for an unknown disease or a known disease considered to pose a non−negligible risk of incursion or emergence. It may also apply to the early stages of an outbreak. early detection HSO:0000271 A surveillance objective focusedon gathering data to estimate the true or apparent prevalence of a hazard in a given population. https://github.com/SVA-SE/AHSURED/wiki This objective is appropriate if the target hazard is (thought to be) present in the territory to be covered, and an assessment of the prevalence and or changes in prevalence over time is needed. prevalence estimation HSO:0000272 https://github.com/SVA-SE/AHSURED/wiki verify health intervention success purpose verify success HSO:0000273 https://github.com/SVA-SE/AHSURED/wiki maintaining hazard freedom purpose maintain freedom HSO:0000274 https://github.com/SVA-SE/AHSURED/wiki detect hazard introduction purpose detect introduction HSO:0000275 https://github.com/SVA-SE/AHSURED/wiki outbreak control purpose control outbreak HSO:0000276 https://github.com/SVA-SE/AHSURED/wiki informing health intervention purpose inform intervention HSO:0000277 https://github.com/SVA-SE/AHSURED/wiki detect changes in hazard occurrence purpose detect changes HSO:0000278 https://github.com/SVA-SE/AHSURED/wiki hazard control purpose control HSO:0000279 https://github.com/SVA-SE/AHSURED/wiki hazard erradication purpose eradicate HSO:0000280 This includes for instance the calculated sample size (which can include primary and secondary sampling units in case of clustered units), the frequency of sampling, etc. A sampling scheme design to meet a specific surveillance objective and/or purpose of a surveillance activity. sampling design protocol HSO:0000281 A reporting protocol, generally used within a surveillance activity, detailing what are the reporting obligations associated with a specific surveillance target in a specific area, the reporting chain (who is obliged to report and how is the information flow from reporting), and any eventual incentives for reporting. reporting protocol HSO:0000282 A protocol detailing how specimens will be collected as part of the data gathering phase of a surveillance activity. sample collection protocol This does not include the definition of how many samples will collected, but specifically how they will be collected - where, by whom, etc. specimen collection protocol HSO:0000283 A protocol that describes which diagnostic test or tests will be used to identify animals (or another epidemiological unit) infected with a specific pathogen, possibly in more than one round of screening. A protocol to be used within a surveillance activity to classify epidemiological units according to a specific outcome. diagnostic protocol HSO:0000284 An action specification for specific actions to be taken as part of a health surveillance activity. surveillance methods specification HSO:0000290 A surveillance context in which sampling in done continuously, triggered by the existing of cases of interest, for instance reporting of confirmed cases or collection of samples from every slaughter batch. https://github.com/SVA-SE/AHSURED/wiki Continuous data collection HSO:0000291 A surveillance context in which data are repeated collected from the same selected sites or groups of animals to identify changes in the health status of a specified population over time. https://github.com/SVA-SE/AHSURED/wiki https://www.fp7-risksur.eu/terminology/glossary Surveillance sentinels should act as a proxy for the larger population of interest; they may be selected on the basis of risk but can also be selected randomly or on the basis of convenience or compliance. Sentinel surveillance HSO:0000292 A surveillance context which explores traditional information networks by using participatory rural appraisal methods. https://github.com/SVA-SE/AHSURED/wiki https://www.fp7-risksur.eu/terminology/glossary Participatory surveillance explores traditional information networks by using participatory rural appraisal methods such as ranking, scoring and visualisation techniques to conduct risk-based, hazard-specific surveillance. The approach uses semi-structured interviews with key informants. This enables communities to provide their knowledge regarding health events, risks, impacts and control opportunities by gathering qualitative health data from defined populations. The analysis of participatory data emphasises the comparison of information obtained from multiple informants; the method uses a variety of techniques to obtain the most likely interpretation of events. The objective is to enhance sensitivity by identifying cases based on a clinical case definition; these may then be evaluated and confirmed using either rapid tests in the field or laboratory diagnostics. Conventional epidemiological investigation techniques can be used to evaluate and confirm outbreaks detected by participatory surveillance as part of trace-back and trace-forwards activities. Participatory surveillance HSO:0000293 A surveillance context in which data are generated through the identification of cases based on agreed-upon definitions. https://github.com/SVA-SE/AHSURED/wiki https://www.fp7-risksur.eu/terminology/glossary Traditional disease surveillance which relies on the collection of data about the occurrence of pre-defined diseases or conditions and which uses agreed-upon case definitions; these data are analysed to produce indicators that point towards the existence of a threat. Indicator-based surveillance may be hazard-specific or general and includes the use of clinical or other data for syndromic surveillance Indicator−based surveillance HSO:0000294 A surveillance context in which health-related information (clinical signs or other data) that might precede or substitute for formal diagnosis are used as indicators of spatio-temporal trends in hazard occurrence. https://github.com/SVA-SE/AHSURED/wiki https://www.fp7-risksur.eu/terminology/glossary#group-S Information collected through syndromic surveillance may be used to indicate a sufficient probability of a change in the health of the population to deserve further investigation or to enable a timely assessment of the impact of health threats which may require action. This type of surveillance is not usually focused on a particular hazard so can be used to detect a variety of diseases or pathogens including new (emerging) diseases. This type of surveillance is particularly applicable for early warning surveillance. Syndromic surveillance HSO:0000314 https://github.com/SVA-SE/AHSURED/wiki census sampling HSO:0000315 https://github.com/SVA-SE/AHSURED/wiki convenience sampling HSO:0000316 https://github.com/SVA-SE/AHSURED/wiki simple random sampling simple random HSO:0000317 https://github.com/SVA-SE/AHSURED/wiki systematic random sampling systematic random HSO:0000318 https://github.com/SVA-SE/AHSURED/wiki risk-based sampling HSO:0000319 https://github.com/SVA-SE/AHSURED/wiki purposeful sampling HSO:0000320 https://github.com/SVA-SE/AHSURED/wiki objective sampling HSO:0000371 A surveillance context in which activities are specifically triggered by the detection of an outbreak outbreak investigation HSO:0000372 a type of outbreak investigation that focus specifically on foodborne agents/vehicles food-borne outbreak investigation HSO:0000373 a surveillance activity with the specific surveillance context of investigating a foodborne outbreak FBO investigation HSO:0000374 a specific type of surveillance activity which has as surveillance context an outbreak investigation Outbreak investigation HSO:0000379 A directive information that described specific detailsgathered during an outbreak investigation. outbreak investigation datum HSO:0000380 Food vehicle of outbreak Food vehicle HSO:0000381 Nature of evidence in an outbreak Nature of evidence HSO:0000382 Outbreak contributory factors Contributory factors HSO:0000383 Extent of outbreak HSO:0000385 A directive information that described the manadatory actions that follow on specific agents upon suspicion or confirmation of specific hazards under surveillance. reporting obligations HSO:0000386 A directive information used to identify diseases which, by law, must be reported to public health authorities upon diagnosis. notifiable upon diagnosis HSO:0000387 A directive information used to identify diseases which, by law, must be reported to public health authorities upon suspicion notifiable upon suspicion HSO:0000388 a quality that specifies the known status of a hazard occurrence in a given geograhial region. status of hazard presence in a geographical region HSO:0000389 historically absent HSO:0000390 absent (eradicated) HSO:0000391 Single cases without a specific temporal pattern, but also without geographical pattern or other associations and where import to location is related to travel. sporadic travel-related cases HSO:0000392 The state of a disease, infection or other condition being maintained in a population without the need of external outputs. The population involved and their geographical location should be specified when defining an endemic state. Present in a community or common among a group of people; said of a disease prevailing continually in a region endemic HSO:0000393 unknown status IAO:0000005 objective specification In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction. a directive information entity that describes an intended process endpoint. When part of a plan specification the concretization is realized in a planned process in which the bearer tries to effect the world so that the process endpoint is achieved. 2009-03-16: original definition when imported from OBI read: "objective is an non realizable information entity which can serve as that proper part of a plan towards which the realization of the plan is directed." 2014-03-31: In the example of usage ("In the protocol of a ChIP assay the objective specification says to identify protein and DNA interaction") there is a protocol which is the ChIP assay protocol. In addition to being concretized on paper, the protocol can be concretized as a realizable entity, such as a plan that inheres in a person. The objective specification is the part that says that some protein and DNA interactions are identified. This is a specification of a process endpoint: the boundary in the process before which they are not identified and after which they are. During the realization of the plan, the goal is to get to the point of having the interactions, and participants in the realization of the plan try to do that. Answers the question, why did you do this experiment? PERSON: Alan Ruttenberg PERSON: Barry Smith PERSON: Bjoern Peters PERSON: Jennifer Fostel goal specification OBI Plan and Planned Process/Roles Branch OBI_0000217 objective specification IAO:0000007 Pour the contents of flask 1 into flask 2 a directive information entity that describes an action the bearer will take Alan Ruttenberg OBI Plan and Planned Process branch action specification IAO:0000027 data item Data items include counts of things, analyte concentrations, and statistical summaries. a data item is an information content entity that is intended to be a truthful statement about something (modulo, e.g., measurement precision or other systematic errors) and is constructed/acquired by a method which reliably tends to produce (approximately) truthful statements. 2/2/2009 Alan and Bjoern discussing FACS run output data. This is a data item because it is about the cell population. Each element records an event and is typically further composed a set of measurment data items that record the fluorescent intensity stimulated by one of the lasers. 2009-03-16: data item deliberatly ambiguous: we merged data set and datum to be one entity, not knowing how to define singular versus plural. So data item is more general than datum. 2009-03-16: removed datum as alternative term as datum specifically refers to singular form, and is thus not an exact synonym. 2014-03-31: See discussion at http://odontomachus.wordpress.com/2014/03/30/aboutness-objects-propositions/ JAR: datum -- well, this will be very tricky to define, but maybe some information-like stuff that might be put into a computer and that is meant, by someone, to denote and/or to be interpreted by some process... I would include lists, tables, sentences... I think I might defer to Barry, or to Brian Cantwell Smith JAR: A data item is an approximately justified approximately true approximate belief PERSON: Alan Ruttenberg PERSON: Chris Stoeckert PERSON: Jonathan Rees data data item IAO:0000030 information content entity Examples of information content entites include journal articles, data, graphical layouts, and graphs. A generically dependent continuant that is about some thing. 2014-03-10: The use of "thing" is intended to be general enough to include universals and configurations (see https://groups.google.com/d/msg/information-ontology/GBxvYZCk1oc/-L6B5fSBBTQJ). information_content_entity 'is_encoded_in' some digital_entity in obi before split (040907). information_content_entity 'is_encoded_in' some physical_document in obi before split (040907). Previous. An information content entity is a non-realizable information entity that 'is encoded in' some digital or physical entity. PERSON: Chris Stoeckert OBI_0000142 information content entity 1 1 IAO:0000032 10 feet. 3 ml. a scalar measurement datum is a measurement datum that is composed of two parts, numerals and a unit label. 2009-03-16: we decided to keep datum singular in scalar measurement datum, as in this case we explicitly refer to the singular form Would write this as: has_part some 'measurement unit label' and has_part some numeral and has_part exactly 2, except for the fact that this won't let us take advantage of OWL reasoning over the numbers. Instead use has measurment value property to represent the same. Use has measurement unit label (subproperty of has_part) so we can easily say that there is only one of them. PERSON: Alan Ruttenberg PERSON: Melanie Courtot scalar measurement datum IAO:0000033 An information content entity whose concretizations indicate to their bearer how to realize them in a process. 2009-03-16: provenance: a term realizable information entity was proposed for OBI (OBI_0000337) , edited by the PlanAndPlannedProcess branch. Original definition was "is the specification of a process that can be concretized and realized by an actor" with alternative term "instruction".It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2013-05-30 Alan Ruttenberg: What differentiates a directive information entity from an information concretization is that it can have concretizations that are either qualities or realizable entities. The concretizations that are realizable entities are created when an individual chooses to take up the direction, i.e. has the intention to (try to) realize it. 8/6/2009 Alan Ruttenberg: Changed label from "information entity about a realizable" after discussions at ICBO Werner pushed back on calling it realizable information entity as it isn't realizable. However this name isn't right either. An example would be a recipe. The realizable entity would be a plan, but the information entity isn't about the plan, it, once concretized, *is* the plan. -Alan PERSON: Alan Ruttenberg PERSON: Bjoern Peters directive information entity IAO:0000100 data set Intensity values in a CEL file or from multiple CEL files comprise a data set (as opposed to the CEL files themselves). A data item that is an aggregate of other data items of the same type that have something in common. Averages and distributions can be determined for data sets. 2009/10/23 Alan Ruttenberg. The intention is that this term represent collections of like data. So this isn't for, e.g. the whole contents of a cel file, which includes parameters, metadata etc. This is more like java arrays of a certain rather specific type 2014-05-05: Data sets are aggregates and thus must include two or more data items. We have chosen not to add logical axioms to make this restriction. person:Allyson Lister person:Chris Stoeckert OBI_0000042 group:OBI data set IAO:0000104 plan specification PMID: 18323827.Nat Med. 2008 Mar;14(3):226.New plan proposed to help resolve conflicting medical advice. A directive information entity with action specifications and objective specifications as parts that, when concretized, is realized in a process in which the bearer tries to achieve the objectives by taking the actions specified. 2009-03-16: provenance: a term a plan was proposed for OBI (OBI_0000344) , edited by the PlanAndPlannedProcess branch. Original definition was " a plan is a specification of a process that is realized by an actor to achieve the objective specified as part of the plan". It has been subsequently moved to IAO where the objective for which the original term was defined was satisfied with the definitionof this, different, term. 2014-03-31: A plan specification can have other parts, such as conditional specifications. Alternative previous definition: a plan is a set of instructions that specify how an objective should be achieved Alan Ruttenberg OBI Plan and Planned Process branch OBI_0000344 2/3/2009 Comment from OBI review. Action specification not well enough specified. Conditional specification not well enough specified. Question whether all plan specifications have objective specifications. Request that IAO either clarify these or change definitions not to use them plan specification IAO:0000109 measurement datum Examples of measurement data are the recoding of the weight of a mouse as {40,mass,"grams"}, the recording of an observation of the behavior of the mouse {,process,"agitated"}, the recording of the expression level of a gene as measured through the process of microarray experiment {3.4,luminosity,}. A measurement datum is an information content entity that is a recording of the output of a measurement such as produced by a device. 2/2/2009 is_specified_output of some assay? person:Chris Stoeckert OBI_0000305 group:OBI measurement datum IAO:0000310 document A journal article, patent application, laboratory notebook, or a book A collection of information content entities intended to be understood together as a whole PERSON: Lawrence Hunter document IAO:0000416 A scalar measurement datum that is the result of measuring a temporal interval 2009/09/28 Alan Ruttenberg. Fucoidan-use-case Person:Alan Ruttenberg time measurement datum IAO:0000572 Recording the current temperature in a laboratory notebook. Writing a journal article. Updating a patient record in a database. A planned process in which a document is created or added to by including the specified input in it. 6/11/9: Edited at OBI workshop. We need to be able identify a child form of information artifact which corresponds to something enduring (not brain like). This used to be restricted to physical document or digital entity as the output, but that excludes e.g. an audio cassette tape Bjoern Peters wikipedia http://en.wikipedia.org/wiki/Documenting documenting IAO:0000582 time stamped measurement datum NCBITaxon:1031542 NCBITaxon:580032 NCBITaxon:580034 GC_ID:11 PMID:19767353 ncbi_taxonomy Campylobacter volucris NCBITaxon:1031919 GC_ID:11 Campylobacter sputorum bv. faecalis ncbi_taxonomy Campylobacter sputorum biovar fecalis Campylobacter sputorum bv. fecalis Campylobacter sputorum biovar faecalis NCBITaxon:1045010 Escherichia coli O157 Escherichia coli O157 NCBITaxon:1055535 Escherichia coli O111 Escherichia coli O111 NCBITaxon:1055536 Escherichia coli O103 Escherichia coli O103 NCBITaxon:1078021 Escherichia coli O113:H21 Escherichia coli O113:H21 NCBITaxon:1078032 Escherichia coli O45:H2 Escherichia coli O45:H2 NCBITaxon:108619 Salmonella enterica subsp. enterica serovar Newport Salmonella enterica subsp. enterica serovar Newport NCBITaxon:1095706 Escherichia coli O18 Escherichia coli O18 NCBITaxon:119231 GC_ID:11 ncbi_taxonomy 'Campylobacter faecalis' Campylobacter faecalis NCBITaxon:1224 Proteobacteria purple bacteria purple bacteria and relatives purple non-sulfur bacteria purple photosynthetic bacteria purple photosynthetic bacteria and relatives Proteobacteria NCBITaxon:1232152 Escherichia coli O103:H11 Escherichia coli O103:H11 NCBITaxon:1244531 NCBITaxon:1244530 NCBITaxon:1442825 NCBITaxon:1442826 NCBITaxon:1442827 GC_ID:11 PMID:25574036 ncbi_taxonomy Campylobacter iguaniorum NCBITaxon:1365258 Escherichia coli 151_06 Escherichia coli 151_06 NCBITaxon:1381117 GC_ID:11 ncbi_taxonomy Campylobacter jejuni X NCBITaxon:1437010 GC_ID:1 PMID:11743200 PMID:11791233 ncbi_taxonomy Boreotheria Boreoeutheria NCBITaxon:1448857 NCBITaxon:1448858 NCBITaxon:1448859 GC_ID:11 PMID:24744327 PMID:24876239 ncbi_taxonomy Campylobacter sp. CIT045 Campylobacter sp. CIT056 Campylobacter sp. CIT058 Campylobacter corcagiensis NCBITaxon:149385 Salmonella enterica subsp. enterica serovar Hadar Salmonella enterica subsp. enterica serovar Hadar NCBITaxon:149539 Salmonella enterica subsp. enterica serovar Enteritidis Salmonella enterica subsp. enterica serovar Enteritidis NCBITaxon:1507806 GC_ID:11 PMID:24336365 PMID:24899653 ncbi_taxonomy Campylobacter fetus subsp. testudinum NCBITaxon:1660067 NCBITaxon:1660068 NCBITaxon:1660069 NCBITaxon:1886620 NCBITaxon:1886621 NCBITaxon:1886668 NCBITaxon:1886669 NCBITaxon:1886671 GC_ID:11 PMID:28629508 ncbi_taxonomy Campylobacter pinnipediorum subsp. pinnipediorum NCBITaxon:1780362 NCBITaxon:1780361 NCBITaxon:1780363 GC_ID:11 PMID:27266587 ncbi_taxonomy Campylobacter geochelonis NCBITaxon:1813019 GC_ID:11 PMID:27498969 ncbi_taxonomy Campylobacter hepaticus NCBITaxon:1848766 GC_ID:11 PMID:28126040 ncbi_taxonomy Campylobacter ornithocola NCBITaxon:1874362 NCBITaxon:1660070 NCBITaxon:1660071 GC_ID:11 PMID:28629508 ncbi_taxonomy Campylobacter pinnipediorum subsp. caledonicus NCBITaxon:192953 Salmonella enterica subsp. enterica serovar Stanley Salmonella enterica subsp. enterica serovar Stanley NCBITaxon:194 Campylobacter GC_ID:11 PMID:11542086 PMID:12361288 PMID:16627635 PMID:1704793 PMID:19801389 PMID:29034857 ncbi_taxonomy Ampylobacter Campylobacter NCBITaxon:195 NCBITaxon:2172530 NCBITaxon:2340791 NCBITaxon:28078 GC_ID:11 PMID:11321120 PMID:11411703 PMID:7857809 PMID:8590689 PMID:9336905 ncbi_taxonomy Campylobacter hyoilei Vibrio coli Campylobacter coli NCBITaxon:196 GC_ID:11 PMID:11321120 PMID:1354478 ncbi_taxonomy Spirillum fetus Vibrio fetus Campylobacter fetus NCBITaxon:1965231 GC_ID:11 PMID:28629508 ncbi_taxonomy Campylobacter pinnipediorum NCBITaxon:197 NCBITaxon:2172531 NCBITaxon:2182326 NCBITaxon:2201165 NCBITaxon:2211407 NCBITaxon:2211408 NCBITaxon:2211409 NCBITaxon:2293848 NCBITaxon:2293849 NCBITaxon:2293850 NCBITaxon:2303571 NCBITaxon:2305452 NCBITaxon:2305453 NCBITaxon:2305454 NCBITaxon:2305455 NCBITaxon:2305456 NCBITaxon:2305457 NCBITaxon:2305458 NCBITaxon:2305459 NCBITaxon:2340789 NCBITaxon:2478524 GC_ID:11 PMID:11321120 ncbi_taxonomy Ampylobacter jejuni Campylobacter fetus subsp. jejuni Vibrio hepaticus Vibrio jejuni Campylobacter jejuni NCBITaxon:198 GC_ID:11 PMID:10425776 PMID:3998100 PMID:7547297 ncbi_taxonomy Campylobacter hyointestinalis NCBITaxon:199 GC_ID:11 PMID:28729281 ncbi_taxonomy Campylobacter concisus NCBITaxon:2 Bacteria eubacteria Bacteria NCBITaxon:200 GC_ID:11 PMID:1704793 PMID:1854636 ncbi_taxonomy Wolinella curva Campylobacter curvus NCBITaxon:201 GC_ID:11 PMID:19406805 PMID:2223613 ncbi_taxonomy Campylobacter laridis Campylobacter lari NCBITaxon:202 GC_ID:11 PMID:11321120 PMID:4614347 ncbi_taxonomy Campylobacter sputorum mucosalis Campylobacter sputorum subsp. mucosalis Campylobacter mucosalis NCBITaxon:203 GC_ID:11 PMID:1704793 PMID:1854636 ncbi_taxonomy Wolinella recta Campylobacter rectus NCBITaxon:204 GC_ID:11 PMID:7694633 ncbi_taxonomy Campylobacter showae NCBITaxon:2042961 NCBITaxon:2044588 GC_ID:11 PMID:29624164 ncbi_taxonomy Campylobacter blaseri NCBITaxon:205 GC_ID:11 ncbi_taxonomy Campylobacter sp. NCBITaxon:206 GC_ID:11 PMID:11321120 PMID:9542089 ncbi_taxonomy Vibrio sputorum Campylobacter sputorum NCBITaxon:207 GC_ID:11 ncbi_taxonomy Campylobacter jejuni-like bacterium NCBITaxon:244317 Escherichia coli O128:H2 Escherichia coli O128:H2 NCBITaxon:244319 Escherichia coli O26:H11 Escherichia coli O26:H11 NCBITaxon:2593542 GC_ID:11 ncbi_taxonomy unclassified Campylobacter NCBITaxon:260714 GC_ID:11 PMID:15545485 ncbi_taxonomy Campylobacter insulaenigrae NCBITaxon:2759 GC_ID:1 PMID:23020233 eucaryotes eukaryotes ncbi_taxonomy Eucarya Eucaryotae Eukarya Eukaryotae eukaryotes Eukaryota NCBITaxon:28079 GC_ID:11 ncbi_taxonomy Campylobacter mucosalis-like sp. Campylobacter mucosalis-like bacterium NCBITaxon:28080 GC_ID:11 ncbi_taxonomy CNW group catalase-negative or weak group of campylobacteria Campylobacter upsaliensis NCBITaxon:28898 GC_ID:11 PMID:1479353 ncbi_taxonomy Campylobacter helveticus NCBITaxon:28901 Salmonella enterica Salmonella enterica NCBITaxon:303118 GC_ID:11 Campylobacter lawrenci ncbi_taxonomy 'Campylobacter lawrenceae ' Campylobacter lawrenceae NCBITaxon:32019 GC_ID:11 PMID:11321120 PMID:12508904 Campylobacter fetus fetus ncbi_taxonomy Vibrio fetus subsp. intestinalis Campylobacter fetus subsp. fetus NCBITaxon:32020 GC_ID:11 PMID:11321120 Campylobacter fetus subsp. venereus Campylobacter fetus venerealis Vibrio foetus venerealis ncbi_taxonomy Vibrio fetus subsp. venerealis Campylobacter fetus subsp. venerealis NCBITaxon:32021 GC_ID:11 PMID:11321120 Campylobacter jejuni doylei ncbi_taxonomy Campylobacter jejuni subsp. doylei NCBITaxon:32022 GC_ID:11 PMID:11321120 Campylobacter jejuni jejuni ncbi_taxonomy Campylobacter jejuni subsp. jejuni NCBITaxon:32023 GC_ID:11 Campylobacter sputorum bubulus ncbi_taxonomy Campylobacter bubulus Vibrio bubulus Campylobacter sputorum subsp. bubulus NCBITaxon:32024 GC_ID:11 PMID:11321120 PMID:9542089 Campylobacter sputorum bv. sputorum Campylobacter sputorum sputorum ncbi_taxonomy Campylobacter sputorum subsp. sputorum Campylobacter sputorum biovar sputorum NCBITaxon:32524 GC_ID:1 amniotes ncbi_taxonomy Amniota NCBITaxon:363569 Salmonella enterica subsp. enterica serovar Javiana Salmonella enterica subsp. enterica serovar Javiana NCBITaxon:374106 NCBITaxon:525139 NCBITaxon:525140 NCBITaxon:525141 NCBITaxon:525142 NCBITaxon:525143 NCBITaxon:525144 NCBITaxon:525145 GC_ID:11 PMID:19542108 ncbi_taxonomy Campylobacter cuniculorum NCBITaxon:376725 Escherichia coli O103:H2 Escherichia coli O103:H2 NCBITaxon:397454 Escherichia coli O142:H6 Escherichia coli O142:H6 NCBITaxon:404394 Escherichia coli O26:NM Escherichia coli O26:NM NCBITaxon:404399 Escherichia coli O26 Escherichia coli O26 NCBITaxon:449520 NCBITaxon:2703845 GC_ID:11 PMID:17978232 ncbi_taxonomy Campylobacter canadensis NCBITaxon:48409 Salmonella enterica subsp. enterica serovar Virchow Salmonella enterica subsp. enterica serovar Virchow NCBITaxon:488545 GC_ID:11 PMID:19406805 ncbi_taxonomy Campylobacter lari subsp. concheus NCBITaxon:488546 GC_ID:11 PMID:19406805 ncbi_taxonomy Campylobacter peloridis NCBITaxon:497724 GC_ID:11 PMID:19661523 ncbi_taxonomy Campylobacter subantarcticus NCBITaxon:522485 NCBITaxon:522483 GC_ID:11 PMID:19620353 ncbi_taxonomy Campylobacter avium NCBITaxon:543 Enterobacteriaceae Enterobacteriaceae NCBITaxon:54736 Salmonella bongori Salmonella bongori NCBITaxon:562 Escherichia coli E. coli Escherichia/Shigella coli Escherichia coli NCBITaxon:590 Salmonella Salmonella NCBITaxon:59201 Salmonella enterica subsp. enterica Salmonella enterica subsp. enterica NCBITaxon:593874 GC_ID:11 Campylobacter sputorum bv. paraureolyticus ncbi_taxonomy Campylobacter sputorum biovar paraureolyticus NCBITaxon:595 Salmonella enterica subsp. enterica serovar Infantis Salmonella enterica subsp. enterica serovar Infantis NCBITaxon:611 Salmonella enterica subsp. enterica serovar Heidelberg Salmonella enterica subsp. enterica serovar Heidelberg NCBITaxon:650054 GC_ID:11 PMID:19406805 ncbi_taxonomy Campylobacter lari subsp. lari NCBITaxon:654363 NCBITaxon:535089 NCBITaxon:654364 NCBITaxon:654365 GC_ID:11 PMID:21278267 ncbi_taxonomy Campylobacter troglodytis NCBITaxon:75658 GC_ID:11 PMID:10758898 ncbi_taxonomy Campylobacter lanienae NCBITaxon:76517 GC_ID:11 PMID:11321111 PMID:7857801 PMID:8123559 PMID:9720027 ncbi_taxonomy Candidatus Campylobacter hominis Campylobacter hominis NCBITaxon:824 GC_ID:11 PMID:1854636 PMID:26383656 PMID:7857794 ncbi_taxonomy Bacteroides gracilis Campylobacter gracilis NCBITaxon:827 GC_ID:11 PMID:1854636 PMID:19801389 PMID:7857794 ncbi_taxonomy Bacteroides corrodens Bacteroides ureolyticus Campylobacter ureolyticus NCBITaxon:9031 GC_ID:1 bantam chicken chickens ncbi_taxonomy Gallus domesticus Gallus gallus domesticus Gallus gallus NCBITaxon:90371 Salmonella enterica subsp. enterica serovar Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium NCBITaxon:91352 GC_ID:11 PMID:10425776 PMID:7547297 ncbi_taxonomy Campylobacter hyointestinalis subsp. hyointestinalis NCBITaxon:91353 GC_ID:11 PMID:10425776 PMID:7547297 ncbi_taxonomy Campylobacter hyointestinalis subsp. lawsonii NCBITaxon:91561 GC_ID:1 whales, hippos, ruminants, pigs, camels etc. ncbi_taxonomy even-toed ungulates Cetartiodactyla NCBITaxon:9606 GC_ID:1 human man ncbi_taxonomy Home sapiens Homo sampiens Homo sapeins Homo sapian Homo sapians Homo sapien Homo sapience Homo sapiense Homo sapients Homo sapines Homo spaiens Homo spiens Humo sapiens Homo sapiens NCBITaxon:9823 GC_ID:1 pig pigs swine wild boar ncbi_taxonomy Sus scrofus Sus scrofa NCBITaxon:98333 GC_ID:11 ncbi_taxonomy Campylobacter cf. lanienae UB 992 NCBITaxon:98336 GC_ID:11 ncbi_taxonomy Campylobacter cf. lanienae UB 994 NCBITaxon:9913 NCBITaxon:272461 GC_ID:1 bovine cattle cow dairy cow domestic cattle domestic cow ncbi_taxonomy Bos Tauurus Bos bovis Bos primigenius taurus Bos taurus NCBITaxon:991913 Escherichia coli O103:H25 Escherichia coli O103:H25 NCBITaxon:991915 Escherichia coli O121:H19 Escherichia coli O121:H19 NCBITaxon:991919 Escherichia coli O145:NM Escherichia coli O145:NM NCIT:C25464 A collective generic term that refers here to a wide variety of dependencies, areas of special sovereignty, uninhabited islands, and other entities in addition to the traditional countries or independent states. COUNTRY Country Country http://purl.obolibrary.org/obo/GEO_000000396 NCIT:C25632 lookup:http://purl.obolibrary.org/obo/GAZ_00000448 A region, district or division of a country; a tract; a portion a state, especially one remote from the capital. Province Province NCIT:C80234 lookup:http://purl.obolibrary.org/obo/GAZ_00000448 A political unit, such as a city, town, or village, incorporated for local self-government. Municipality Municipality http://semanticscience.org/resource/SIO_000665 NCIT:C87194 lookup:http://purl.obolibrary.org/obo/GAZ_00000448 A constituent administrative district of a nation. State Territory State NCIT:C89811 lookup:http://purl.obolibrary.org/obo/GAZ_00000448 A geographical area under the jurisdiction of a sovereign state and marked off for administrative or other purposes. Territory Territory OBI:0000011 planned process planned process Injecting mice with a vaccine in order to test its efficacy A processual entity that realizes a plan which is the concretization of a plan specification. 'Plan' includes a future direction sense. That can be problematic if plans are changed during their execution. There are however implicit contingencies for protocols that an agent has in his mind that can be considered part of the plan, even if the agent didn't have them in mind before. Therefore, a planned process can diverge from what the agent would have said the plan was before executing it, by adjusting to problems encountered during execution (e.g. choosing another reagent with equivalent properties, if the originally planned one has run out.) We are only considering successfully completed planned processes. A plan may be modified, and details added during execution. For a given planned process, the associated realized plan specification is the one encompassing all changes made during execution. This means that all processes in which an agent acts towards achieving some objectives is a planned process. Bjoern Peters branch derived 6/11/9: Edited at workshop. Used to include: is initiated by an agent This class merges the previously separated objective driven process and planned process, as they the separation proved hard to maintain. (1/22/09, branch call) planned process OBI:0000066 investigation Lung cancer investigation using expression profiling, a stem cell transplant investigation, biobanking is not an investigation, though it may be part of an investigation a planned process that consists of parts: planning, study design execution, documentation and which produce conclusion(s). Bjoern Peters OBI branch derived Could add specific objective specification Following OBI call November 2012,26th: it was decided there was no need for adding "achieves objective of drawing conclusion" as existing relations were providing equivalent ability. this note closes the issue and validates the class definition to be part of the OBI core editor = PRS study investigation OBI:0000070 assay Assay the wavelength of light emitted by excited Neon atoms. Count of geese flying over a house. A planned process with the objective to produce information about the material entity that is the evaluant, by physically examining it or its proxies. 12/3/12: BP: the reference to the 'physical examination' is included to point out that a prediction is not an assay, as that does not require physical examiniation. PlanAndPlannedProcess Branch measuring scientific observation OBI branch derived study assay any method assay OBI:0000112 specimen role liver section; a portion of a culture of cells; a nemotode or other animal once no longer a subject (generally killed); portion of blood from a patient. a role borne by a material entity that is gained during a specimen collection process and that can be realized by use of the specimen in an investigation 22Jun09. The definition includes whole organisms, and can include a human. The link between specimen role and study subject role has been removed. A specimen taken as part of a case study is not considered to be a population representative, while a specimen taken as representing a population, e.g. person taken from a cohort, blood specimen taken from an animal) would be considered a population representative and would also bear material sample role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. blood taken from animal: animal continues in study, whereas blood has role specimen. something taken from study subject, leaves the study and becomes the specimen. parasite example - when parasite in people we study people, people are subjects and parasites are specimen - when parasite extracted, they become subject in the following study specimen can later be subject. GROUP: Role Branch OBI specimen role OBI:0000245 organization PMID: 16353909.AAPS J. 2005 Sep 22;7(2):E274-80. Review. The joint food and agriculture organization of the United Nations/World Health Organization Expert Committee on Food Additives and its role in the evaluation of the safety of veterinary drug residues in foods. An entity that can bear roles, has members, and has a set of organization rules. Members of organizations are either organizations themselves or individual people. Members can bear specific organization member roles that are determined in the organization rules. The organization rules also determine how decisions are made on behalf of the organization by the organization members. BP: The definition summarizes long email discussions on the OBI developer, roles, biomaterial and denrie branches. It leaves open if an organization is a material entity or a dependent continuant, as no consensus was reached on that. The current placement as material is therefore temporary, in order to move forward with development. Here is the entire email summary, on which the definition is based: 1) there are organization_member_roles (president, treasurer, branch editor), with individual persons as bearers 2) there are organization_roles (employer, owner, vendor, patent holder) 3) an organization has a charter / rules / bylaws, which specify what roles there are, how they should be realized, and how to modify the charter/rules/bylaws themselves. It is debatable what the organization itself is (some kind of dependent continuant or an aggregate of people). This also determines who/what the bearer of organization_roles' are. My personal favorite is still to define organization as a kind of 'legal entity', but thinking it through leads to all kinds of questions that are clearly outside the scope of OBI. Interestingly enough, it does not seem to matter much where we place organization itself, as long as we can subclass it (University, Corporation, Government Agency, Hospital), instantiate it (Affymetrix, NCBI, NIH, ISO, W3C, University of Oklahoma), and have it play roles. This leads to my proposal: We define organization through the statements 1 - 3 above, but without an 'is a' statement for now. We can leave it in its current place in the is_a hierarchy (material entity) or move it up to 'continuant'. We leave further clarifications to BFO, and close this issue for now. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Philippe Rocca-Serra PERSON: Susanna Sansone GROUP: OBI organization OBI:0000260 plan The plan of researcher X to perform an experiment according to a protocol. A plan is a realizable entity that is the inheres in a bearer who is committed to realizing it as a planned process. This class is included to make clear how the plan specification, the plan, and the planned process relate. OBI will however only subclass and work under the 'plan specification', and 'planned process' class, as we want to avoid to get deep into discussions of 'intend' etc. AR, BP, JM, MC, PRS branch derived plan OBI:0000272 protocol PCR protocol, has objective specification, amplify DNA fragment of interest, and has action specification describes the amounts of experimental reagents used (e..g. buffers, dNTPS, enzyme), and the temperature and cycle time settings for running the PCR. A plan specification which has sufficient level of detail and quantitative information to communicate it between investigation agents, so that different investigation agents will reliably be able to independently reproduce the process. PlanAndPlannedProcess Branch OBI branch derived + wikipedia (http://en.wikipedia.org/wiki/Protocol_%28natural_sciences%29) study protocol protocol OBI:0000338 interpreting data Concluding that a gene is upregulated in a tissue sample based on the band intensity in a western blot. Concluding that a patient has a infection based on measurement of an elevated body temperature and reported headache. Concluding that there were problems in an investigation because data from PCR and microarray are conflicting. Concluding that 'defects in gene XYZ cause cancer due to improper DNA repair' based on data from experiments in that study that gene XYZ is involved in DNA repair, and the conclusion of a previous study that cancer patients have an increased number of mutations in this gene. A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion PERSON: Bjoern Peters PERSON: Jennifer Fostel Bjoern Peters drawing a conclusion based on data OBI:0000339 planning The process of a scientist thinking about and deciding what reagents to use as part of a protocol for an experiment. Note that the scientist could be human or a "robot scientist" executing software. a process of creating or modifying a plan specification 7/18/2011 BP: planning used to itself be a planned process. Barry Smith pointed out that this would lead to an infinite regression, as there would have to be a plan to conduct a planning process, which in itself would be the result of planning etc. Therefore, the restrictions on 'planning' were loosened to allow for informal processes that result in an 'ad hoc plan '. This required changing from 'has_specified_output some plan specifiction' to 'has_participant some plan specification'. Bjoern Peters Bjoern Peters Plans and Planned Processes Branch planning OBI:0000471 study design execution injecting a mouse with PBS solution, weighing it, and recording the weight according to a study design. a planned process that carries out a study design removed axiom has_part some (assay or 'data transformation') per discussion on protocol application mailing list to improve reasoner performance. The axiom is still desired. branch derived 6/11/9: edited at workshop. Used to be: study design execution is a process with the objective to generate data according to a concretized study design. The execution of a study design is part of an investigation, and minimally consists of an assay or data transformation. study design execution OBI:0000659 specimen collection process drawing blood from a patient for analysis, collecting a piece of a plant for depositing in a herbarium, buying meat from a butcher in order to measure its protein content in an investigation A planned process with the objective of collecting a specimen. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. Philly2013: A specimen collection can have as part a material entity acquisition, such as ordering from a bank. The distinction is that specimen collection necessarily involves the creation of a specimen role. However ordering cell lines cells from ATCC for use in an investigation is NOT a specimen collection, because the cell lines already have a specimen role. Philly2013: The specimen_role for the specimen is created during the specimen collection process. label changed to 'specimen collection process' on 10/27/2014, details see tracker: http://sourceforge.net/p/obi/obi-terms/716/ Bjoern Peters specimen collection 5/31/2012: This process is not necessarily an acquisition, as specimens may be collected from materials already in posession 6/9/09: used at workshop specimen collection process OBI:0000684 specimen collection objective The objective to collect bits of excrement in the rainforest. The objective to obtain a blood sample from a patient. A objective specification to obtain a material entity for potential use as an input during an investigation. Bjoern Peters Bjoern Peters specimen collection objective OBI:0000844 hospital human ethics approval was obtained from the Southern Tasmania Health & Medical Human Research Ethics Committee and the Royal Hobart Hospital Research Ethics Committee [pmid:19696660] A medical organization at which sick or injured people are given clinical care Person:Alan Ruttenberg Person:Helen Parkinson http://www.golovchenko.org/cgi-bin/wnsearch?q=hospital#2n modified from the wording of the wordnet definition 2009/09/28 Alan Ruttenberg. Fucoidan-use-case hospital OBI:0001909 The conclusion that a gene is upregulated in a tissue sample based on the band intensity in a western blot. The conclusion that a patient has a infection based on measurement of an elevated body temperature and reported headache. The conclusion that there were problems in an investigation because data from PCR and microarray are conflicting. The following are NOT conclusions based on data: data themselves; results from pure mathematics, e.g. "13 is prime". An information content entity that is inferred from data. In the Philly 2013 workshop, we recognized the limitations of "conclusion textual entity", and we introduced this as more general. The need for the 'textual entity' term going forward is up for future debate. Group:2013 Philly Workshop group Group:2013 Philly Workshop group conclusion based on data OBI:0002897 surveillance process An investigation in which some entity is monitored, and data concerning that entity collected, interpreted, and disseminated, for the purpose of managing, directing, or protecting that entity, or some other entity. Chris Stoeckert Shane Babcock, OBI https://github.com/obi-ontology/obi/issues/1181 IDO, VEuPathDB surveillance process OBI:0100026 organism animal fungus plant virus A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs. 10/21/09: This is a placeholder term, that should ideally be imported from the NCBI taxonomy, but the high level hierarchy there does not suit our needs (includes plasmids and 'other organisms') 13-02-2009: OBI doesn't take position as to when an organism starts or ends being an organism - e.g. sperm, foetus. This issue is outside the scope of OBI. GROUP: OBI Biomaterial Branch WEB: http://en.wikipedia.org/wiki/Organism organism OBI:0100051 specimen Biobanking of blood taken and stored in a freezer for potential future investigations stores specimen. A material entity that has the specimen role. Note: definition is in specimen creation objective which is defined as an objective to obtain and store a material entity for potential use as an input during an investigation. PERSON: James Malone PERSON: Philippe Rocca-Serra GROUP: OBI Biomaterial Branch specimen OBI:0500000 study design a matched pairs study design describes criteria by which subjects are identified as pairs which then undergo the same protocols, and the data generated is analyzed by comparing the differences between the paired subjects, which constitute the results of the executed study design. A plan specification comprised of protocols (which may specify how and what kinds of data will be gathered) that are executed as part of an investigation and is realized during a study design execution. Editor note: there is at least an implicit restriction on the kind of data transformations that can be done based on the measured data available. PERSON: Chris Stoeckert experimental design rediscussed at length (MC/JF/BP). 12/9/08). The definition was clarified to differentiate it from protocol. study design The part of the pancreas that is part of the exocrine system and which produces and store zymogens of digestive enzymes, such as chymotrypsinogen and trypsinogen in the acinar cells [GO]. The exocrine pancreas is composed of acinar epithelial cells and ductal epithelium that manufacture the proteolytic enzymes and bicarbonate required for digestion.[TAO] The part of the pancreas that acts as an exocrine gland, consisting of the pancreatic acini, which produce pancreatic juice and secrete it into the intestine to aid in protein digestion. [TFD][VHOG] In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] AAO:0010407 BTO:0000434 CALOHA:TS-1241 EMAPA:35328 EV:0100093 FMA:16017 MA:0002415 NCIT:C32546 TAO:0001249 UMLS:C0553695 VHOG:0000048 XAO:0000137 ZFA:0001249 exocrine pancreas pars exocrina pancreatis uberon exocrine component of pancreas exocrine part of pancreas UBERON:0000017 exocrine pancreas UBERON:0000017 An organ that is capable of transducing sensory stimulus to the nervous system. AEO:0000094 BSA:0000121 BTO:0000202 CALOHA:TS-2043 EHDAA2:0001824 EHDAA:500 EMAPA:35955 FBbt:00005155 GAID:63 HAO:0000930 MA:0000017 MESH:D012679 NCIT:C33224 UMLS:C0935626 VHOG:0001407 WBbt:0006929 organ of sense organ system organ of sensory organ system organ of sensory system sense organ system organ sensory organ sensory organ system organ sensory system organ sensillum uberon Sinnesorgan sensor UBERON:0000020 sense organ UBERON:0000020 Any of the rounded masses of lymphoid tissue that are surrounded by a capsule of connective tissue, are distributed along the lymphatic vessels, and contain numerous lymphocytes which filter the flow of lymph. Lymph nodes that are associated with the lymphatic system have evolved in mammals.[well established][VHOG] BTO:0000784 CALOHA:TS-0579 EFO:0000872 EMAPA:35523 EV:0100050 FMA:5034 GAID:947 MA:0000139 MAT:0000442 MESH:D008198 NCIT:C12745 NCIT:C33027 OpenCyc:Mx4rwLPqLpwpEbGdrcN5Y29ycA TAO_RETIRED:0005318 UMLS:C0024204 VHOG:0001273 ZFA_RETIRED:0005318 galen:Lymphnode uberon lymph gland nodus lymphaticus UBERON:0000029 lymph node UBERON:0000029 A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]. Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] AAO:0010396 BTO:0000706 CALOHA:TS-1306 EFO:0000840 EMAPA:19252 EV:0100077 FMA:7201 GAID:306 MA:0000333 MESH:A03.492.411.495 MIAA:0000046 NCIT:C12379 OpenCyc:Mx4rvVkF5pwpEbGdrcN5Y29ycA UMLS:C0021851 VHOG:0000054 XAO:0000131 galen:LargeIntestine uberon intestinum crassum UBERON:0000059 large intestine UBERON:0000059 cjm A subdivision of the digestive tract that connects the small intestine to the cloaca or anus. Lacks or has few villi[Kardong]. ISBN10:0073040584 Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] 2012-09-17 VHOG:0000054 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566 UMLS:C0021851 ncithesaurus:Large_Intestine intestinum crassum BTO:0000706 Material anatomical entity that is a single connected structure with inherent 3D shape generated by coordinated expression of the organism's own genome. AAO:0010825 AEO:0000003 BILA:0000003 CARO:0000003 EHDAA2:0003003 EMAPA:0 FBbt:00007001 FMA:305751 FMA:67135 GAID:781 HAO:0000003 MA:0003000 MESH:D000825 TAO:0000037 TGMA:0001823 VHOG:0001759 XAO:0003000 ZFA:0000037 biological structure connected biological structure uberon UBERON:0000061 anatomical structure UBERON:0000061 Anatomical structure that performs a specific function or group of functions [WP]. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions. CARO v1 does not include a generic 'organ' class, only simple and compound organ. CARO v2 may include organ, see https://github.com/obophenotype/caro/issues/4 CARO:0020004 EFO:0000634 EMAPA:35949 ENVO:01000162 FMA:67498 MA:0003001 NCIT:C13018 OpenCyc:Mx4rv5XMb5wpEbGdrcN5Y29ycA OpenCyc:Mx4rwP3iWpwpEbGdrcN5Y29ycA UMLS:C0178784 WBbt:0003760 uberon anatomical unit body organ element UBERON:0000062 organ UBERON:0000062 A multicellular structure that is a part of an organ. currently defined in a very broad sense, may be replaced by more specific classes in the future AAO:0011124 EFO:0000635 FMA:82472 cardinal organ part uberon regional part of organ UBERON:0000064 organ part UBERON:0000064 A glycoprotein membrane surrounding the plasma membrane of an oocyte. It is a vital constitutive part of the latter, external but not extraneous to it. The zona pellucida first appears in multilaminar primary oocytes. Outside the plasma membrane, three envelopes surround the ovum. The first, the primary egg envelope, lies between the plasma membrane and the surrounding cells of the ovary. The most consistent component of this primary layer is the vitelline membrane, a transparent jacket of fibrous protein. In mammals, the homologous structure is called the zona pellucida.[well established][VHOG] zona pellucida - vitelline membrane BTO:0003135 EHDAA2:0002220 EHDAA:31 EHDAA:62 EMAPA:16035 FMA:18674 GAID:410 MA:0001715 MESH:D015044 NCIT:C33896 TAO:0001111 UMLS:C0043519 VHOG:0000720 ZFA:0001111 uberon oolemma pellucid zone striated membrane vitelline envelope vitelline membrane zona radiata zona striata UBERON:0000086 zona pellucida UBERON:0000086 Nonparenchymatous organ that primarily consists of dense connective tissue organized into a sheet which interconnects two or more organs, separates two or more body spaces from one another, or surrounds an organ or body part. Examples: interosseous membrane of forearm, obturator membrane, tympanic membrane, fibrous pericardium, fascia lata, dura mater. [FMA] cjm 2009-07-30T05:19:13Z membrane FMA:7145 membrane of organ uberon UBERON:0000094 membrane organ UBERON:0000094 Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. This class is probably too inclusive Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO] The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] intestinal In zebrafish, No stomach, small intestine, or large intestine can be distinguished. However, differences can be found in the morphology of the mucosa columnar epithelial cells and the number of goblet cells, suggesting functional differentiation. The intestine has numerous folds that become progressively shorter in a rostral-to-caudal direction. Proportionally, these folds are significantly larger than the finger-like intestinal villi of mammals and other amniotes (Wallace et al. 2005). Columnar-shaped absorptive enterocytes are the most numerous in the zebrafish intestinal epithelium. Goblet cells are the second most populous epithelial cell type. AAO:0000246 ANISEED:1235303 BSA:0000093 BTO:0000648 CALOHA:TS-0490 EFO:0000834 EMAPA:32874 EV:0100071 FMA:7199 GAID:295 MA:0000328 MA:0001524 MESH:A03.492.411 MIAA:0000043 NCIT:C12736 TAO:0001338 UMLS:C0021853 VHOG:0000056 WBbt:0005772 XAO:0000129 ZFA:0001338 galen:Intestine bowel uberon intestinal tract UBERON:0000160 intestine UBERON:0000160 cjm Segment of the alimentary canal extending from the stomach to the anus and, in humans and other mammals, consists of two segments, the small intestine and the large intestine. GOC:GO Portion of the alimentary canal bounded anteriorly by the pyloric sphincter and posteriorly by the cloacal sphincter.[AAO] 2012-06-20 AAO:0000246 AAO AAO:EJS The tract of the alimentary canal. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000056 VHOG UMLS:C0021853 ncithesaurus:Intestine 1 1 1 1 The pair of anatomical structures comprised of a left lung and right lung. FMA:68877 OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA lungs lungs pair pulmones set of lungs uberon UBERON:0000170 pair of lungs UBERON:0000170 Organ that functions in gaseous exchange between an organism and its environment. In plants, microorganisms, and many small animals, air or water makes direct contact with the organism's cells or tissue fluids, and the processes of diffusion supply the organism with dioxygen (O2) and remove carbon dioxide (CO2). In larger animals the efficiency of gaseous exchange is improved by specialized respiratory organs, such as lungs and gills, which are ventilated by breathing mechanisms. EMAPA:17607 SPD:0000428 TGMA:0001247 apparatus respiratorius organ breathing organ organ of apparatus respiratorius organ of respiratory system respiratory organ respiratory system organ uberon gas exchange organ UBERON:0000171 respiration organ UBERON:0000171 A portion of organism substance that is the product of an excretion process that will be eliminated from the body. An excretion process is elimination by an organism of the waste products that arise as a result of metabolic activity UBERON:0000324 UBERON:0007550 AEO:0000184 BTO:0000491 EHDAA2_RETIRED:0003184 ENVO:02000022 FMA:9674 galen:Excretion excreted substance portion of excreted substance waste substance uberon excretion UBERON:0000174 excreta UBERON:0000174 A fluid that is composed of blood plasma and erythrocytes. This class excludes blood analogues, such as the insect analog of blood. See UBERON:0000179 haemolymphatic fluid. A complex mixture of cells suspended in a liquid matrix that delivers nutrients to cells and removes wastes. (Source: BioGlossary, www.Biology-Text.com)[TAO] Highly specialized circulating tissue consisting of several types of cells suspended in a fluid medium known as plasma.[AAO] relationship loss: subclass specialized connective tissue (AAO:0000571)[AAO] Recent findings strongly suggest that the molecular pathways involved in the development and function of blood cells are highly conserved among vertebrates and various invertebrates phyla. (...) There is now good reason to believe that, in vertebrates and invertebrates alike, blood cell lineages diverge from a common type of progenitor cell, the hemocytoblast.[well established][VHOG] AAO:0000046 BTO:0000089 CALOHA:TS-0079 EFO:0000296 EHDAA2:0000176 EHDAA:418 EMAPA:16332 ENVO:02000027 EV:0100047 FMA:9670 GAID:965 MA:0000059 MESH:D001769 MIAA:0000315 NCIT:C12434 OpenCyc:Mx4rvVjI8JwpEbGdrcN5Y29ycA TAO:0000007 UMLS:C0005767 VHOG:0000224 XAO:0000124 ZFA:0000007 galen:Blood portion of blood vertebrate blood uberon whole blood UBERON:0000178 blood UBERON:0000178 Circulating fluid that is part of the hemolymphoid system. Blood, lymph, interstitial fluid or its analogs. cjm 2009-04-08T04:38:19Z CARO:0000081 uberon blood or blood analog circulating fluid UBERON:0000179 haemolymphatic fluid UBERON:0000179 An embryo that is at the late embryonic stage; this stage covers late steps of the embryogenesis with a fully formed embryo still developing before birth or egg hatching. TODO - check fetus/embryo. WP: An embryo is a multicellular diploid eukaryote in its earliest stage of development, from the time of first cell division until birth, hatching, or germination. In humans, it is called an embryo until about eight weeks after fertilization (i.e. ten weeks LMP), and from then it is instead called a fetus. Fetal structure, which is a developmental form of a vertebrate animal at any given time point from 8 weeks of gestation to birth (or hatching). Examples: There is only one fetus[FMA:63919]. BTO:0000449 CALOHA:TS-0360 EFO:0001323 FBbt:00005333 FMA:63919 GAID:552 MESH:D005333 NCIT:C13235 OpenCyc:Mx4rvZfC2ZwpEbGdrcN5Y29ycA UMLS:C0015965 fetus uberon embryo late growth stage embryo late stage UBERON:0000323 late embryo UBERON:0000323 The branched tubular glands found in the mucosa of the fundus and body of the stomach which contain parietal cells that secrete hydrochloric acid and zymogenic cells that produce pepsin. BTO:0000503 EMAPA:27181 FMA:14919 uberon UBERON:0000325 gastric gland UBERON:0000325 A gland in which the principal secretory cells are serous secreting cells. glands that secrete watery albuminous material that often contains enzymes[MP:0008052]. BTO:0001837 EMAPA:37950 FMA:62889 uberon UBERON:0000409 serous gland UBERON:0000409 A gland in which the principal secretory cells are mucus secreting cells. In frogs and salamanders, this is the smaller of the two types of gland, the other being the granular (poison) gland. In these species the mucous gland is a cluster of cells that release secretion into a common duct[Kardong] AAO:0010601 BTO:0001979 EMAPA:37913 FMA:62888 glandula mucosa uberon muciparous gland mucous secreting gland mucus gland mucus-secreting gland UBERON:0000414 mucous gland UBERON:0000414 A portion of organism substance that is produced by exocrine glands. BTO has two distunct classes, with exocrine glandular secretion a subtype of secretion - however, all examples in BTO directly under secretion appear to be exocrine gland secretions UBERON:0006540 secretion AEO:0001005 BTO:0002977 BTO:0002979 EMAPA:36535 FMA:9675 MA:0002504 MESH:D012634 NCIT:C34062 UMLS:C1516992 galen:Secretion bodily secretion exocrine gland fluid/secretion secreted substance uberon exocrine gland fluid exocrine gland fluid or secretion exocrine gland secretion external secretion UBERON:0000456 secretion of exocrine gland UBERON:0000456 Material anatomical entity in a gaseous, liquid, semisolid or solid state; produced by anatomical structures or derived from inhaled and ingested substances that have been modified by anatomical structures as they pass through the body. AAO:0010839 AEO:0000004 BILA:0000004 CALOHA:TS-2101 CARO:0000004 EHDAA2:0003004 EMAPA:35178 FBbt:00007019 FMA:9669 HAO:0000004 MA:0002450 NCIT:C13236 SPD:0000008 TAO:0001487 TGMA:0001824 VHOG:0001726 XAO:0004001 ZFA:0001487 galen:BodySubstance body fluid or substance body substance organism substance portion of body substance portion of organism substance uberon UBERON:0000463 organism substance UBERON:0000463 Anatomical entity that has mass. AAO:0010264 AEO:0000006 BILA:0000006 CARO:0000006 EHDAA2:0003006 FBbt:00007016 FMA:67165 HAO:0000006 TAO:0001836 TGMA:0001826 VHOG:0001721 uberon UBERON:0000465 material anatomical entity UBERON:0000465 Multicellular, connected anatomical structure that has multiple organs as parts and whose parts work together to achieve some shared function. system AAO:0000007 AEO:0000011 BILA:0000011 BSA:0000049 CALOHA:TS-2088 CARO:0000011 EHDAA2:0003011 EHDAA:392 EMAPA:16103 EV:0100000 FBbt:00004856 FMA:7149 HAO:0000011 MA:0000003 NCIT:C12919 OpenCyc:Mx4rCWM0QCtDEdyAAADggVbxzQ TAO:0001439 TGMA:0001831 UMLS:C0460002 VHOG:0001725 WBbt:0005746 WBbt:0005763 XAO:0003002 ZFA:0001439 galen:AnatomicalSystem body system connected anatomical system organ system uberon anatomical systems UBERON:0000467 anatomical system UBERON:0000467 Anatomical structure that is an individual member of a species and consists of more than one cell. TODO - split body and mc organism? body continues after death stage organismal organism AAO:0010026 AEO:0000191 BILA:0000012 BSA:0000038 BTO:0000042 CARO:0000012 EFO:0002906 EHDAA2:0003103 EHDAA2:0003191 EHDAA:1 EMAPA:25765 EV:0100016 FBbt:00000001 FMA:256135 HAO:0000012 NCIT:C13041 TADS:0000001 TAO:0001094 TGMA:0001832 VHOG:0000671 WBbt:0007833 XAO:0003004 ZFA:0001094 galen:Organism ncithesaurus:Whole_Organism multi-cellular organism animal uberon Koerper body whole body whole organism UBERON:0000468 multicellular organism UBERON:0000468 The organs and associated structures associated with bearing offspring in a female animal. By far, sexual reproduction is the more common pattern among living vertebrate forms and its widespread occurrence suggests that it is the plesiomorphic, or primitive, reproductive mode among the vertebrates.[well established][VHOG] BTO:0000083 CALOHA:TS-1303 EFO:0000969 EHDAA2:0000506 EHDAA:8116 EMAPA:17959 EV:0100110 FBbt:00004864 FMA:45663 GAID:364 HAO:0000324 MA:0000381 MESH:D005836 MIAA:0000028 NCIT:C12402 OpenCyc:Mx4rvVipTZwpEbGdrcN5Y29ycA TGMA:0000635 UMLS:C0700038 VHOG:0000726 WBbt:0006748 WikipediaCategory:Female_reproductive_system XAO:0000156 female organism genitalia female organism reproductive system genitalia of female organism reproductive system of female organism uberon female genital system female genital tract female genitalia female genitals female reproductive tract gynaecological tissue systema genitale femininum UBERON:0000474 female reproductive system UBERON:0000474 Anatomical structure that consists of cell parts and cell substances and together does not constitute a cell or a tissue. AAO:0010268 AEO:0000040 BILA:0000040 CARO:0000040 EHDAA2:0003040 FBbt:00007013 FMA:63863 HAO:0000040 TAO:0000382 TGMA:0001841 XAO:0003162 ZFA:0000382 uberon acellular anatomical structures UBERON:0000476 acellular anatomical structure UBERON:0000476 Multicellular anatomical structure that consists of many cells of one or a few types, arranged in an extracellular matrix such that their long-range organisation is at least partly a repetition of their short-range organisation. changed label and definition to reflect CARO2 AAO:0000607 AAO:0010054 AEO:0000043 BILA:0000043 CALOHA:TS-2090 CARO:0000043 EHDAA2:0003043 EMAPA:35868 FBbt:00007003 FMA:9637 HAO:0000043 MA:0003002 MESH:D014024 NCIT:C12801 TAO:0001477 TGMA:0001844 UMLS:C0040300 VHOG:0001757 WBbt:0005729 XAO:0003040 ZFA:0001477 galen:Tissue portion of tissue tissue portion simple tissue uberon UBERON:0000479 tissue UBERON:0000479 Anatomical structure that has as its parts two or more portions of tissue of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona-fide boundaries from other distinct structural units of different types. AAO:0010048 AEO:0000055 BILA:0000055 CARO:0000055 EHDAA2:0003055 FBbt:00007010 HAO:0000055 TAO:0001488 TGMA:0001847 VHOG:0001762 XAO:0003037 ZFA:0001488 uberon multi-tissue structures UBERON:0000481 multi-tissue structure UBERON:0000481 Compound organ that contains one or more macroscopic anatomical spaces. this class was introduced for consistency with CARO, however, it has yet to be used in this or other ontologies. It may be retired in the future AAO:0010016 AEO:0000072 BILA:0000072 CARO:0000072 EHDAA2:0003072 FMA:55671 HAO:0000072 TAO:0001490 TGMA:0001857 VHOG:0001730 XAO:0003165 ZFA:0001490 cavitated organ uberon cavitated compound organs UBERON:0000489 cavitated compound organ UBERON:0000489 Mucus is a bodily fluid consisting of a slippery secretion of the lining of the mucous membranes in the body. It is a viscous colloid containing antiseptic enzymes (such as lysozyme) and immunoglobulins. Mucus is produced by goblet cells in the mucous membranes that cover the surfaces of the membranes. It is made up of mucins and inorganic salts suspended in water. mucoid mucous CALOHA:TS-2144 ENVO:02000040 FMA:66938 GAID:1164 MESH:D009093 NCIT:C13259 OpenCyc:Mx4rvVjHq5wpEbGdrcN5Y29ycA UMLS:C0026727 galen:Mucus uberon UBERON:0000912 mucus UBERON:0000912 Interstitial fluid is a bodily fluid consisting of a solution which bathes and surrounds the cells of multicellular animals. It is the main component of the extracellular fluid, which also includes plasma and transcellular fluid. ENVO:02000042 FMA:9673 NCIT:C120839 intercellular fluid tissue fluid uberon UBERON:0000913 interstitial fluid UBERON:0000913 Anatomical entity that comprises the organism in the early stages of growth and differentiation that are characterized by cleavage, the laying down of fundamental tissues, and the formation of primitive organs and organ systems. For example, for mammals, the process would begin with zygote formation and end with birth. For insects, the process would begin at zygote formation and end with larval hatching. For plant zygotic embryos, this would be from zygote formation to the end of seed dormancy. For plant vegetative embryos, this would be from the initial determination of the cell or group of cells to form an embryo until the point when the embryo becomes independent of the parent plant. embryonic Obsoleted in ZFA. Note that embryo is not classified as an embryonic structure - an embryonic structure is only the parts of an embryo AAO:0011035 AEO:0000169 BILA:0000056 BSA:0000039 BTO:0000379 CALOHA:TS-0229 EFO:0001367 EHDAA2:0000002 EHDAA2_RETIRED:0003236 EHDAA:38 EMAPA:16039 FBbt:00000052 FMA:69068 GAID:963 MAT:0000226 MESH:D004622 MIAA:0000019 NCIT:C28147 OGEM:000001 OpenCyc:Mx4rwP1ceZwpEbGdrcN5Y29ycA UMLS:C0013935 VHOG:0001766 XAO:0000113 ZFA:0000103 embryonic organism uberon developing organism developmental tissue UBERON:0000922 embryo UBERON:0000922 An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO] It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG] We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa AAO:0000579 ANISEED:1235297 BTO:0001307 CALOHA:TS-0980 EFO:0000837 EHDAA2:0001915 EHDAA:2993 EMAPA:17021 EV:0100070 FMA:7148 GAID:293 MA:0000353 MAT:0000051 MESH:A03.492.766 MIAA:0000051 NCIT:C12391 OpenCyc:Mx4rvVjlqpwpEbGdrcN5Y29ycA TAO:0002121 UMLS:C0038351 VHOG:0000408 XAO:0000128 galen:Stomach stomach chamber uberon anterior intestine gaster mesenteron ventriculus UBERON:0000945 stomach UBERON:0000945 cjm cjm An expanded region of the vertebrate alimentary tract that serves as a food storage compartment and digestive organ. A stomach is lined, in whole or in part by a glandular epithelium. ISBN10:0073040584 Portion of alimentary canal with increased circular and longitudinal smooth muscle. Bounded posteriorly by the pyloric sphincter. Mucosal lining has increased folding.[AAO] 2012-06-20 AAO:0000579 AAO AAO:EJS It appears that the stomach has an ancient origin. The stomach first appears in the fish lineage. The prevertebrate chordates do not have a true stomach, whereas the cartilaginous and bony fish do. Although most fish do have a true stomach, some fish species appear to have lost the stomach secondarily. The remaining vertebrate lineages do have a true stomach (at least in the adult animal), although there is great variation in the size and shape of the stomach.[well established][VHOG] 2012-09-17 VHOG:0000408 VHOG DOI:10.1046/j.1525-142x.2000.00076.x Smith DM, Grasty RC, Theodosiou NA, Tabin CJ, Nascone-Yoder NM, Evolutionary relationships between the amphibian, avian, and mammalian stomachs. Evolution and development (2000) We restrict this to the vertebrate specific structure - see the grouping class 'food storage organ' for analogous structures in other species. Teleosts: Zebrafish is functionally stomach-less, but may retain ontogenic footprint. Although the precise shape and size of the stomach varies widely among different vertebrates, the relative positions of the oesophageal and duodenal openings remain relatively constant. As a result, the organ always curves somewhat to the left before curving back to meet the pyloric sphincter. However, lampreys, hagfishes, chimaeras, lungfishes, and some teleost fish have no stomach at all, with the oesophagus opening directly into the intestine. The gastric lining is usually divided into two regions, an anterior portion lined by fundic glands, and a posterior with pyloric glands. Cardiac glands are unique to mammals, and even then are absent in a number of species. The distributions of these glands vary between species, and do not always correspond with the same regions as in man. Furthermore, in many non-human mammals, a portion of the stomach anterior to the cardiac glands is lined with epithelium essentially identical to that of the oesophagus. Ruminants, in particular, have a complex stomach, the first three chambers of which are all lined with oesophageal mucosa WP:Stomach#In_other_animals UMLS:C0038351 ncithesaurus:Stomach gaster BTO:0001307 ventriculus Anatomical system that consists of the glands and parts of glands that produce endocrine secretions and help to integrate and control bodily metabolic activity. Anatomical system containing glands which regulates bodily functions though the secretion of hormones.[AAO] Multicellular organisms have complex endocrine systems, allowing responses to environmental stimuli, regulation of development, reproduction, and homeostasis. Nuclear receptors (NRs), a metazoan-specific family of ligand-activated transcription factors, play central roles in endocrine responses, as intermediates between signaling molecules and target genes. The NR family includes ligand-bound and orphan receptors, that is, receptors with no known ligand or for which there is no ligand Pocket. Understanding NR evolution has been further improved by comparison of several completed genomes, particularly those of deuterostomes and ecdysozoans. In contrast, evolution of NR ligands is still much debated. One hypothesis proposes that several independent gains and losses of ligand-binding ability in NRs occurred in protostomes and deuterostomes. A second hypothesis, pertaining to the NR3 subfamily (vertebrate steroid hormone receptors and estrogen related receptor), proposes that before the divergence of protostomes and deuterostomes, there was an ancestral steroid receptor (AncSR) that was ligand-activated and that orphan receptors secondarily lost the ability to bind a ligand. (...) Our analysis reveals that steroidogenesis has been independently elaborated in the 3 main bilaterian lineages (...).[well established][VHOG] endocrine AAO:0010279 CALOHA:TS-1301 EFO:0002969 EHDAA2:0002224 EMAPA:35306 EV:0100128 FBbt:00005068 FMA:9668 GAID:439 MA:0000012 MESH:D004703 NCIT:C12705 TAO:0001158 UMLS:C0014136 VHOG:0000098 XAO:0000158 ZFA:0001158 endocrine glandular system endocrine system systema endocrinum uberon UBERON:0000949 endocrine system UBERON:0000949 The brain is the center of the nervous system in all vertebrate, and most invertebrate, animals. Some primitive animals such as jellyfish and starfish have a decentralized nervous system without a brain, while sponges lack any nervous system at all. In vertebrates, the brain is located in the head, protected by the skull and close to the primary sensory apparatus of vision, hearing, balance, taste, and smell[WP]. requires review for applicability to invertebrate structures, e.g. synganglion Cavitated compound organ which is comprised of gray and white matter and surrounds the cerebral ventricular system.[TAO] Part of the central nervous system situated within the cranium and composed of both nerve cell bodies and nerve fibers.[AAO] The part of the central nervous system contained within the cranium, comprising the forebrain, midbrain, hindbrain, and metencephalon. It is derived from the anterior part of the embryonic neural tube (or the encephalon). Does not include retina. (CUMBO) (...) at some stage of its development, every chordate exhibits five uniquely derived characters or synapomorphies of the group: (...) (4) a single, tubular nerve cord that is located dorsal to the notochord (...) (reference 1); The neural tube is destined to differentiate into the brain and spinal cord (the central nervous system) (reference 2).[well established][VHOG] AAO:0010478 ABA:Brain BAMS:Br BAMS:Brain BILA:0000135 BTO:0000142 CALOHA:TS-0095 DHBA:10155 EFO:0000302 EHDAA2:0000183 EHDAA:2641 EHDAA:6485 EMAPA:16894 EV:0100164 FBbt:00005095 FMA:50801 GAID:571 HBA:4005 MA:0000168 MAT:0000098 MBA:8 MBA:997 MESH:D001921 MIAA:0000098 NCIT:C12439 OpenCyc:Mx4rvVjT65wpEbGdrcN5Y29ycA PBA:3999 TAO:0000008 UMLS:C0006104 UMLS:C1269537 VHOG:0000157 XAO:0000010 ZFA:0000008 galen:Brain http://braininfo.rprc.washington.edu/centraldirectory.aspx?ID=21 uberon encephalon suprasegmental levels of nervous system suprasegmental structures synganglion the brain UBERON:0000955 brain UBERON:0000955 Anatomical system that has as its parts the organs concerned with reproduction. consider splitting genitalia from reproductive system Anatomical system which consists of organs and tissues associated with sexual reproduction of the organism.[AAO] Arguably, one of the most important aspects of urbilaterian organogenesis would have been gonadogenesis, since Urbilateria must have successfully generated gametes and developed a strategy for extrusion and fertilization, in order to be the ancestor of all living Bilateria.[well established][VHOG] AAO:0010258 BILA:0000103 BTO:0000081 CALOHA:TS-1318 EFO:0000809 EHDAA2:0001603 EHDAA:5923 EMAPA:17381 EV:0100100 FBbt:00004857 FMA:7160 GAID:363 HAO:0000374 HAO:0000895 MA:0000326 MIAA:0000305 NCIT:C12841 OpenCyc:Mx4rvVja4ZwpEbGdrcN5Y29ycA TAO:0000632 UMLS:C1261210 VHOG:0000182 WBbt:0005747 XAO:0000142 ZFA:0000632 uberon Geschlechtsorgan animal reproductive system genital system genital tract genitalia organa genitalia reproductive tissue reproductive tract systemata genitalia UBERON:0000990 reproductive system UBERON:0000990 Functional system which consists of structures involved in respiration. The anatomical system in which the exchange of oxygen and carbon dioxide between the organism and its environment.[AAO] There is no doubt that the primitive pattern of vertebrate air-breathing is the buccal pulse pump found in actinopterygian fishes.[well established][VHOG] AAO:0000541 BTO:0000203 CALOHA:TS-1319 EFO:0000804 EHDAA2:0001604 EHDAA:2203 EMAPA:16727 EV:0100036 FMA:7158 GAID:78 MA:0000327 MAT:0000030 MESH:D012137 MIAA:0000030 NCIT:C12779 OpenCyc:Mx4rvVjzFJwpEbGdrcN5Y29ycA TAO:0000272 UMLS:C0035237 VHOG:0000202 XAO:0000117 ZFA:0000272 apparatus respiratorius respiratory system uberon Atmungssystem apparatus respiratorius systema respiratorium UBERON:0001004 respiratory system UBERON:0001004 Anatomical system that has as its parts the organs devoted to the ingestion, digestion, and assimilation of food and the discharge of residual wastes. An anatomical system consisting of the alimentary canal and digestive glands responsible for intake, absorption, digestion and excretion of food.[AAO] digestive many anatomy ontologies consider gastrointestinal system synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class AAO:0000129 BILA:0000082 BTO:0000058 CALOHA:TS-1293 EFO:0000793 EV:0100056 FBbt:00005055 FMA:7152 GAID:278 MA:0002431 MAT:0000018 MESH:D004064 MIAA:0000018 TADS:0000170 TAO:0000339 WBbt:0005748 XAO:0000125 ZFA:0000339 galen:DigestiveSystem ncithesaurus:Digestive_System uberon alimentary system alimentary tract gastrointestinal system gut UBERON:0001007 digestive system UBERON:0001007 The renal system in an anatomical system that maintains fluid balance and contributes to electrolyte balance, acid/base balance, and disposal of nitrogenous waste products.. In various sources such as Encyclopedia Britannica, the excretory and urinary systems are indeed the same system (see wikipedia talk page); we merge two BTO classes here An anatomical system which consists of organs and tissues which produce, store, and excrete urine.[AAO] Evolution of vertebrate renal anatomy appears quite conservative when compared, for example, to evolution of respiratory and cardiovascular systems in vertebrates. Major anatomical changes in vertebrates kidneys separate those of birds and mammals from kidneys of lower vertebrates. General increase in animal size from fish to mammals is reflected by an increase in total number of nephrons per kidney, rather than by constant change in tubular dimensions.[well established][VHOG] In humans, the renal system comprises a pair of kidneys, a pair of ureters, urinary bladder, urethra, sphincter muscle and associated blood vessels This definition is inclusive of the organs of the vertebrate renal system, as well as the Malpighian tubules of insects, and allows for future incorporation of structures such as the antennal glands of crustaceans AAO:0010257 BILA:0000015 BTO:0001244 BTO:0003092 CALOHA:TS-1323 EFO:0000803 EHDAA2:0001601 EHDAA:5901 EMAPA:17366 EV:0100095 FBbt:00005056 FMA:7159 GAID:391 MA:0000325 MAT:0000027 MESH:D014551 MIAA:0000027 NCIT:C12413 TADS:0000162 TAO:0000163 UMLS:C1508753 VHOG:0000723 WBbt:0005736 XAO:0000143 ZFA:0000163 galen:UrinaryTract excretory system renal system systema urinaria systema urinarium urinary system urinary tract uberon renal or urinary system renal/urinary system UBERON:0001008 renal system UBERON:0001008 organ system that passes nutrients (such as amino acids and electrolytes), gases, hormones, blood cells, etc. to and from cells in the body to help fight diseases and help stabilize body temperature and pH to maintain homeostasis[WP]. the cardiovascular system and the lymphatic system are parts of the circulatory system Anatomical system of ion binding, a pumping mechanism, and an efficient vascular system; consisting of the blood, heart, and blood and lymph vessels, respectively.[AAO] We should divest ourselves of the view that earlier vertebrate groups were 'on their way' to becoming mammals, as clearly they were not such visionaries. Neither were their systems 'imperfect' as earlier anatomists thought. Instead, their circulatory systems served them well to address the ecological demands arising from their lifestyles.[well established][VHOG] AAO:0000959 CALOHA:TS-2103 FBbt:00005057 OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA VHOG:0001248 uberon systema cardiovasculare UBERON:0001009 circulatory system UBERON:0001009 The nervous system is an organ system containing predominantly neuron and glial cells. In bilaterally symmetrical organism, it is arranged in a network of tree-like structures connected to a central body. The main functions of the nervous system are to regulate and control body functions, and to receive sensory input, process this information, and generate behavior [CUMBO]. A regulatory system of the body that consists of neurons and neuroglial cells. The nervous system is divided into two parts, the central nervous system (CNS) and the peripheral nervous system (PNS). (Source: BioGlossary, www.Biology-Text.com)[TAO] Anatomical system consisting of nerve bodies and nerve fibers which regulate the response of the body to external and internal stimuli.[AAO] Nervous systems evolved in the ancestor of Eumetazoa.[well established][VHOG] nervous neural AAO:0000324 BILA:0000079 BTO:0001484 CALOHA:TS-1313 EFO:0000802 EHDAA2:0001246 EHDAA:826 EMAPA:16469 EV:0100162 FBbt:00005093 FMA:7157 GAID:466 MA:0000016 MAT:0000026 MESH:D009420 MIAA:0000026 NCIT:C12755 OpenCyc:Mx4rvViT_pwpEbGdrcN5Y29ycA TAO:0000396 UMLS:C0027763 VHOG:0000402 WBbt:0005735 XAO:0000177 ZFA:0000396 neurological system nerve net uberon systema nervosum UBERON:0001016 nervous system UBERON:0001016 Anatomical system that overlaps the nervous system and is responsible for receiving and processing sensory information. An early step in the evolution of neural crest, therefore, may have been the origin of a specific dorsal neural cell population contributing to sensory processing; this would predate the divergence of the amphioxus and vertebrate lineages.[well established][VHOG] note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs AAO:0000555 BAMS:SEN BILA:0000099 EFO:0000805 EHDAA2:0003094 EMAPA:16192 FBbt:00007692 FMA:75259 MA:0002442 MAT:0000031 MIAA:0000031 TAO:0000282 VHOG:0001674 XAO:0003194 ZFA:0000282 organa sensuum sense organ subsystem sense organs sense organs set sensory subsystem sensory systems uberon organa sensuum sensory organ system set of sense organs UBERON:0001032 sensory system UBERON:0001032 Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993). Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO] The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG] esophageal esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995) AAO:0000145 ANISEED:1235301 BTO:0000959 CALOHA:TS-0700 EFO:0000835 EHDAA2:0001285 EHDAA:2937 EMAPA:16833 EV:0100069 FMA:7131 GAID:291 MA:0000352 MAT:0000048 MESH:A03.365 MIAA:0000048 NCIT:C12389 OpenCyc:Mx4rvVj9Q5wpEbGdrcN5Y29ycA TAO:0000204 UMLS:C0014876 VHOG:0000450 XAO:0000127 ZFA:0000204 galen:Esophagus gullet oesophagus uberon UBERON:0001043 esophagus UBERON:0001043 Tube that connects the pharynx to the stomach. In mammals, the oesophagus connects the buccal cavity with the stomach. The stratified squamous non-keratinised epithelium lining the buccal cavity is continued through the pharynx down into the oesophagus. The lowest part of the oesophagus (ca. 2 cm) is lined with gastric mucosa and covered by peritoneum. The main body of the oesophagus is lined with small, simple mucous glands. Each gland opens into the lumen by a long duct which pierces the muscularis mucosae (Wilson and Washington, 1989). A sphincter is situated at the point where the oesophagus enters the stomach to prevent gastro-oesophageal reflux, i.e. to prevent acidic gastric contents from reaching stratified epithelia of the oesophagus, where they can cause inflammation and irritation (Wilson and Washington, 1989; Brown et al., 1993). Anterior end of the alimentary canal lined with smooth muscle. Bounded anteriorly by a constriction in the pharynx. Bounded posteriorly by and increase in circular and/or longitudinal smooth muscle associated with the stomach.[AAO] 2012-06-20 AAO:0000145 AAO AAO:EJS The few structural specializations in (adult lampreys) pharynx include complex valves on the external gill openings that direct the tidal flow, and the division of the ancestral pharynx into an oesophagus and a respiratory pharynx.[well established][VHOG] 2012-09-17 VHOG:0000450 VHOG DOI:10.1111/j.1096-3642.1996.tb01658.x Mallatt J, Ventilation and the origin of jawed vertebrates: a new mouth. Zoological Journal of the Linnean Society (1996) esophagus NOT part of gut in MA. part of gut in ZFA. part_of gut (via UGIT) in FMA. Consider splitting. Interspecies: The human oesophagus is 25 cm long and has a diameter of ca. 2 cm. Only little information was found on the oesophagus in rat, rabbit and pig. The oesophagus of rat (75 x 2 mm) and rabbit has no mucous glands and the cardia of the stomach has a well-developed sphincter, which prevents them from vomiting (Hebel and Stromberg, 1988; Manning et al., 1994). Morphologically the oesophagus is similar in man and pig; both are omnivores and have a non-keratinised epithelium, submucous glands and similar membrane enzymes. Like in humans, pigs can suffer from reflux oesophagitis and stress ulceration of the oesophagus. The pig oesophagus may therefore be a good model for investigation compared to the human oesophagus (Christie et al., 1995) MA UMLS:C0014876 ncithesaurus:Esophagus the terminal portion of the intestinal tube, terminating with the anus The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] rectal In the lungfish, sharks and rays the rectum opens into the cloaca which also receives wastes (urine) from the kidneys and material from the reproductive organs. In bony fish the rectum reaches the outside environment through the anus, which is normally situated just in front the urinary and reproductive openings. However in some fish the digestive tract may be curled back on itself, and in the Electric Eel (Electrophorus electricus) the anus is situated in the fish's throat. -- http://www.earthlife.net/fish/digestion.html AAO:0010401 BTO:0001158 CALOHA:TS-1180 EFO:0000848 EHDAA2:0001592 EHDAA:5836 EMAPA:17896 EV:0100081 FMA:14544 GAID:311 MA:0000336 MAT:0000050 MESH:A03.492.411.495.767 MIAA:0000050 NCIT:C12390 OpenCyc:Mx4rvVjaU5wpEbGdrcN5Y29ycA UMLS:C0034896 VHOG:0001751 XAO:0000238 galen:Rectum terminal portion of intestine uberon intestinum rectum rectal sac terminal portion of large intestine UBERON:0001052 rectum UBERON:0001052 4 cjm MA ISBN10:0073040584 the terminal portion of the intestinal tube, terminating with the anus ISBN:0-683-40008-8 MP:0000492 The terminal portion of the large intestine between the ileo-pelvic colon and the anus. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0001751 VHOG UMLS:C0034896 ncithesaurus:Rectum intestinum rectum BTO:0001158 Biological entity that is either an individual member of a biological species or constitutes the structural organization of an individual member of a biological species. AAO:0010841 AEO:0000000 BILA:0000000 CARO:0000000 EHDAA2:0002229 FBbt:10000000 FBbt_root:00000000 FMA:62955 HAO:0000000 MA:0000001 NCIT:C12219 TAO:0100000 TGMA:0001822 UMLS:C1515976 WBbt:0000100 XAO:0000000 ZFA:0100000 uberon UBERON:0001062 anatomical entity UBERON:0001062 Joint fluid is a transudate of plasma that is actively secreted by synovial cells. Portion of organism substance that is a clear fluid that occupies the space in synovial joints.[TAO] It provides nutrients and lubrication for articular cartilage The fluid contains hyaluronan secreted by fibroblast-like cells in the synovial membrane, lubricin (proteoglycan 4; PRG4) secreted by the surface chondrocytes of the articular cartilage and interstitial fluid filtered from the blood plasma BTO:0001339 CALOHA:TS-0996 ENVO:02000039 FMA:12277 GAID:265 MA:0002544 MESH:D013582 NCIT:C33718 TAO:0005154 UMLS:C0039097 ZFA:0005154 galen:SynovialFluid joint fluid uberon UBERON:0001090 synovial fluid UBERON:0001090 A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction. caecal A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates. BTO:0000166 CALOHA:TS-0122 EFO:0000850 EHDAA2:0000206 EHDAA:3913 EMAPA:35197 EV:0100397 FMA:14541 GAID:307 MA:0000334 MESH:A03.492.411.495.209 MIAA:0000288 NCIT:C12381 OpenCyc:Mx4rve6u4JwpEbGdrcN5Y29ycA UMLS:C0007531 VHOG:0001559 galen:Cecum caecum cecum intestinum crassum caecum caeca ceca uberon blind intestine blindgut intestinum caecum intestinum crassum cecum UBERON:0001153 Kardong: in some herbivorous lizards, a cecum is present between small and large intestines caecum UBERON:0001153 EHDAA2 A pouch in the digestive tract that connects the ileum with the ascending colon of the large intestine. It is separated from the ileum by the ileocecal valve, and is the beginning of the large intestine. It is also separated from the colon by the cecocolic junction. A cecum is present in most amniote species, and also in lungfish, but not in any living species of amphibian. In reptiles, it is usually a single median structure, arising from the dorsal side of the large intestine. Birds typically have two paired ceca, as, unlike other mammals, do hyraxes. Most mammalian herbivores have a relatively large cecum, hosting a large number of bacteria, which aid in the enzymatic breakdown of plant materials such as cellulose; in many species, it is considerably wider than the colon. In contrast, obligatory carnivores, whose diets contain little or no plant material, have a reduced cecum, which is often partially or wholly replaced by the vermiform appendix. Many fish have a number of small outpocketings, called pyloric ceca, along their intestine; despite the name they are not homologous with the cecum of amniotes, and their purpose is to increase the overall area of the digestive epithelium.[2] Some invertebrates, such as squid,[3] may also have structures with the same name, but these have no relationship with those of vertebrates. WP UMLS:C0007531 ncithesaurus:Cecum caecum VHOG:0001559 cecum FMA:14541 caeca NCBITaxon:8782 ceca NCBITaxon:8782 blind intestine BTO:0000166 blindgut BTO:0000166 intestinum caecum BTO:0000166 intestinum crassum cecum BTO:0000166 Last portion of the large intestine before it becomes the rectum. TODO - abstract this such that it legitimately covers all vertebrates The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO] The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO] Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] colonic In mammals, the colon consists of four sections: the ascending colon, the transverse colon, the descending colon, and the sigmoid colon[WP] In zebrafish, the posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates[ZFIN] it extracts water and salt from solid wastes before they are eliminated from the body[WP] AAO:0010400 BTO:0000269 CALOHA:TS-0158 EFO:0000361 EMAPA:18939 EV:0100079 FMA:14543 GAID:309 MA:0000335 MAP:0000001 MAT:0000526 MESH:A03.492.411.495.356 NCIT:C12382 OpenCyc:Mx4rvgLEM5wpEbGdrcN5Y29ycA TAO:0000706 UMLS:C0009368 VHOG:0000648 XAO:0000243 ZFA:0000706 galen:Colon large bowel posterior intestine uberon hindgut UBERON:0001155 colon UBERON:0001155 3 cjm FMA Last portion of the large intestine before it becomes the rectum. ZFIN:curator The last portion of the digestive system, it extracts water and salt from solid wastes before they are eliminated from the body.[AAO] 2012-06-20 AAO:0010400 AAO UBERON:0001155 The posterior intestine has short longitudinally arranged epithelial folds which are similar to the colon of higher vertebrates. Wallace et al, 2005.[TAO] 2012-08-14 TAO:0000706 TAO ZFIN:curator Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000648 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 UMLS:C0009368 ncithesaurus:Colon A complex network of conduits that begins with the canals of Hering (intralobar bile duct) and progressively merges into a system of interlobular, septal, and major ducts which then coalesce to form the extrahepatic bile ducts, which finally deliver bile to the intestine, and in some species to the gallbladder. Hollow tree organ, the organ parts of which consist of the bile ducts.[AAO] AAO:0011020 EMAPA:35172 FMA:14665 UMLS:C0005423 XAO:0000455 uberon biliary tract UBERON:0001173 The path in many species is as follows: Bile canaliculi -> Canals of Hering (intralobar bile duct) -> interlobular bile ducts -> intrahepatic bile ducts -> left and right hepatic ducts merge to form -> common hepatic duct *exits liver* and joins -> cystic duct (from gall bladder) forming -> common bile duct -> joins with pancreatic duct -> forming ampulla of Vater -> enters duodenum [WP] biliary tree UBERON:0001173 An endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes[GO]. Organ which secretes a fluid containing enzymes that aid in the digestion of food.[AAO] In the hagfish and lampreys (our most primitive vertebrate species of today), the first sign of 'a new organ' is found as collections of endocrine cells around the area of the bile duct connection with the duodenum. These endocrine organs are composed of 99% beta cells and 1% somatostatin-producing delta cells. Compared to the more primitive protochordates (e.g. amphioxus), this represents a stage where all previously scattered insulin-producing cells of the intestinal tissue have now quantitatively migrated to found a new organ involved in sensing blood glucose rather than gut glucose. Only later in evolution, the beta cells are joined by exocrine tissue and alpha cells (exemplified by the rat-, rabbit- and elephant-fishes). Finally, from sharks and onwards in evolution, we have the islet PP-cell entering to complete the pancreas.[well established][VHOG] pancreatic As a secretory organ serving exocrine and endocrine functions, the pancreas is specific to the vertebrates[PMID:16417468] Hagfishes and lampreys are unique in the complete separation of their endocrine pancreas (islet or- gan) and their exocrine pancreas (50). The endocrine and exocrine pancreas are coassociated in crown gnathostomes (50). In Branchiostoma and Ciona, there is no diverticulum as there is in hagfishes, lampreys, and gnathostomes, only dispersed insulin-secreting cells in the walls of the gastrointestinal tract (51, 52) The zebrafish does not have a discrete pancreas. Exocrine pancreatic tissue can be found scattered along the intestinal tract. The acinar structure of the exocrine pancreas is very similar to that of mammals and comprises cells with a very dark, basophilic cytoplasm The mature pancreas of higher vertebrates and mammals comprises two major functional units: the exocrine pancreas, which is responsible for the production of digestive enzymes to be secreted into the gut lumen, and the endocrine pancreas, which has its role in the synthesis of several hormones with key regulatory functions in food uptake and metabolism. The exocrine portion constitutes the majority of the mass of the pancreas, and contains only two different cell types, the secretory acinar cells and the ductular cells. The endocrine portion, which comprises only 1-2% of the total mass, contains five different cell types, which are organized into mixed functional assemblies referred to as the islets of Langerhans AAO:0010112 BTO:0000988 CALOHA:TS-0736 EFO:0000855 EHDAA2:0001367 EHDAA:6893 EMAPA:17503 EV:0100092 FMA:7198 GAID:334 MA:0000120 MAT:0000075 MESH:D010179 MIAA:0000075 NCIT:C12393 OpenCyc:Mx4rvVimZZwpEbGdrcN5Y29ycA TAO:0000140 UMLS:C0030274 VHOG:0000050 XAO:0000136 ZFA:0000140 galen:Pancreas uberon UBERON:0001264 pancreas UBERON:0001264 An articular capsule (or joint capsule) is an envelope surrounding a synovial joint. [WP,unvetted]. check ncita EMAPA:37621 FMA:34836 GAID:263 MA:0001519 MESH:D017746 NCIT:C32259 NCIT:C84388 UMLS:C0206207 galen:JointCapsule capsula articularis fibrous capsule of joint joint capsule joint fibrous capsule uberon capsulae articulares UBERON:0001484 articular capsule UBERON:0001484 A specialized accessory gland of the skin of mammals that secretes milk. The gland is typically only developed in females, and regresses in males. Originally this was classified as a female reproductive structure, as it was in the MP in 2011 Any of the milk-producing apocrine glands typically occurring in pairs in female mammals and consisting of lobes containing clusters of alveoli with a system of ducts to convey the milk to an external nipple or teat. [TFD][VHOG] The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG] mammary A mouse mammary gland contains a single duct or sinus, forming 5-10 secondary ducts The male Dayak fruit bat has lactating mammary glands The mammary glands of humans are in the thoracid/breast region. In other mammals they may be located elsewhere on the mammary ridges. The BTO class represents the combination of nipple plus lobe The FMA class represents an individule lobe. The nipple is not a part The MA class represents a composite structure, including the nipple, fat, connective tissue, smooth muscle as parts BTO:0000817 CALOHA:TS-0595 EFO:0000854 EMAPA:17759 EV:0100125 FMA:286452 MA:0000145 MAT:0000073 MESH:D008321 MIAA:0000073 NCIT:C12367 OpenCyc:Mx4rvVjVq5wpEbGdrcN5Y29ycA UMLS:C0929301 VHOG:0000398 glandula mammaria lactiferous gland lobe of breast milk patch uberon Brustdruese dug glandula mammaria lobe of mammary gland mamma mammae UBERON:0001911 mammary gland UBERON:0001911 An emulsion of fat globules within a fluid that is secreted by the mammary gland during lactation. to axiomatize the different forms of mammary gland secretion an ontology of the phases of pregnancy/lactation is required. Using the existing GO def of lactation is circular. The detailed similarities of mammary glands in living monotremes, marsupials, and eutherians argue for a monophyletic origin of these glands, perhaps by the combination of parts of preexisting sebaceous and sweat glands.[well established][VHOG] ncit:Milk refers specifically to cow milk BTO:0000868 CALOHA:TS-0636 EMAPA:36540 ENVO:02000031 EV:0100126 FMA:62100 GAID:1230 MA:0002552 MAT:0000056 MESH:A13.622 MIAA:0000056 NCIT:C13401 OpenCyc:Mx4rvVjGZJwpEbGdrcN5Y29ycA UMLS:C1511310 VHOG:0001263 galen:Milk mammary gland milk uberon UBERON:0001913 milk UBERON:0001913 The liquid component of blood, in which erythrocytes are suspended. plasma portion of plasma BTO:0000131 CALOHA:TS-0800 EFO:0001905 EMAPA:35690 FMA:62970 GAID:1178 MA:0002501 MAT:0000052 MESH:D010949 MIAA:0000052 NCIT:C13356 OpenCyc:Mx4rEg4ZYrIbEduAAAAOpmP6tw UMLS:C0032105 blood plasm portion of blood plasma uberon UBERON:0001969 blood plasma UBERON:0001969 vital aqueous secretion of the liver that is formed by hepatocytes and modified down stream by absorptive and secretory properties of the bile duct epithelium. In many species, bile is stored in the gallbladder and upon eating is discharged into the duodenum. aids the process of digestion of lipids in the small intestine bile salts function to emulsify dietary fats and facilitate their intestinal absorption elimination of cholesterol major excretory route for potentially harmful exogenous lipophilic substances many hormones and pheromones are excreted in bile, and contribute to growth and development of the intestine in some species and provide attractants for the weaning of non-human vertebrates protects the organism from enteric infections by excreting immune globulin A (IgA), inflammatory cytokines, and stimulating the innate immune system in the intestine BTO:0000121 CALOHA:TS-1172 ENVO:02000023 FMA:62971 GAID:1157 MA:0002513 MESH:D001646 NCIT:C13192 UMLS:C0005388 ZFA:0005857 galen:Bile uberon fel gall UBERON:0001970 bile UBERON:0001970 organ of metabolic interchange between fetus and mother, partly of embryonic origin and partly of maternal origin[GO]. The fetal portion of the placenta is known as the villous chorion. The maternal portion is known as the decidua basalis. The two portions are held together by anchoring villi that are anchored to the decidua basalis by the cytotrophoblastic shell. Phylogenetic analyses of the concatenated data set using maximum parsimony, maximum likelihood and distance based (neighbour joining) methods all converged on a nearly identical, well supported topology defining four principal eutherian lineages. The results affirm monophyly of traditional placental orders (except Artiodactyla and Insectivora), and also support some previously proposed, as well as new, superordinal clades.[well established][VHOG] placental Eutherians: In eutherians, the chorioallantoic membrane of the fetus establishes intimate contact with the adjacent vascular wall of the mother's uterus to produce the placenta, a composite structure formed in part from tissues of the fetus and in part from tissues of the mother [ISBN10:0073040584 (Vertebrates, Kardong)]. TODO - is taxon restriction too strict, even if we restrict def to allantoic placenta? - WP says: also found in some snakes and lizards with varying levels of development up to mammalian levels. Pough et al. 1992. Herpetology: Third Edition. Pearson Prentice Hall:Pearson Education, Inc., 2002. // See also: http://dx.doi.org/10.1002/jmor.11011 BTO:0001078 CALOHA:TS-0799 EFO:0001407 EMAPA:35689 EV:0100119 FMA:63934 GAID:379 MA:0000386 MAT:0000279 MESH:A16.759 MIAA:0000279 NCIT:C13272 OpenCyc:Mx4rvv4zZ5wpEbGdrcN5Y29ycA UMLS:C0032043 VHOG:0001266 allantoic placenta eutherian placenta uberon UBERON:0001987 Marsupials possess only a rudimentary yolk-type placenta, with reduced nutrient and oxygen exchanging capabilities. placenta UBERON:0001987 Portion of semisolid bodily waste discharged through the anus[MW,modified] Excretion in semisolid state processed by the intestine.[FMA] fecal excreta BTO:0000440 CALOHA:TS-2345 ENVO:00002003 FMA:64183 GAID:1199 MA:0002509 MAT:0000053 MESH:D005243 MIAA:0000053 NCIT:C13234 OpenCyc:Mx4rvVjJMZwpEbGdrcN5Y29ycA UMLS:C0015733 galen:Feces faeces fecal material fecal matter matières fécales@fr merde@fr partie de la merde@fr piece of shit porción de mierda@es portion of excrement portion of faeces portion of fecal material portion of fecal matter portion of feces portionem cacas stool teil der fäkalien@de cow dung cow pat dung fewmet frass guano portion of dung portion of guano portion of scat scat spraint uberon droppings excrement ordure spoor UBERON:0001988 feces UBERON:0001988 Respiration organ that develops as an oupocketing of the esophagus. Either of two organs which allow gas exchange absorbing oxygen from inhaled air and releasing carbon dioxide with exhaled air.[AAO] Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata. (...) In actinopterygian fishes, apart from Cladistia, the ventral intestinal pocket migrates dorsally and becomes the swim-bladder, a mainly hydrostatical organ (reference 1); Comparative transcriptome analyses indicate molecular homology of zebrafish swimbladder and Mammalian lung (reference 2).[well established][VHOG] pulmonary respiration organ in all air-breathing animals, including most tetrapods, a few fish and a few snails. In mammals and the more complex life forms, the two lungs are located in the chest on either side of the heart. Their principal function is to transport oxygen from the atmosphere into the bloodstream, and to release carbon dioxide from the bloodstream into the atmosphere. This exchange of gases is accomplished in the mosaic of specialized cells that form millions of tiny, exceptionally thin-walled air sacs called alveoli. // Avian lungs do not have alveoli as mammalian lungs do, they have Faveolar lungs. They contain millions of tiny passages known as para-bronchi, connected at both ends by the dorsobronchi AAO:0000275 AAO:0010567 BTO:0000763 CALOHA:TS-0568 EFO:0000934 EHDAA2:0001042 EHDAA:1554 EHDAA:2205 EMAPA:16728 EV:0100042 FMA:7195 GAID:345 MA:0000415 MAT:0000135 MESH:D008168 MIAA:0000135 NCIT:C12468 OpenCyc:Mx4rvVjKy5wpEbGdrcN5Y29ycA UMLS:C0024109 VHOG:0000310 XAO:0000119 galen:Lung pulmo uberon UBERON:0002048 Snakes and limbless lizards typically possess only the right lung as a major respiratory organ; the left lung is greatly reduced, or even absent. Amphisbaenians, however, have the opposite arrangement, with a major left lung, and a reduced or absent right lung [WP] lung UBERON:0002048 Anatomical structure that is part of an embryo. Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[AAO] Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[TAO] Anatomical structure that is part of the embryo and is comprised of portions of tissue or cells.[VSAO] in FMA embryo is_a embryonic structure AAO:0000138 BILA:0000034 BTO:0000174 CALOHA:TS-2110 EFO:0000461 FBbt:00004208 FMA:69067 GAID:407 MESH:D004628 NCIT:C13229 RETIRED_EHDAA2:0003169 TAO:0001105 UMLS:C0013948 VSAO:0000178 XAO:0003042 ZFA:0001105 developing embryonic structure embryonic anatomical structure uberon developing structure embryonale Struktur embryonic structures UBERON:0002050 embryonic structure UBERON:0002050 An organ that is located within the body cavity (or in its extension, in the scrotum); it consists of organ parts that are embryologically derived from endoderm, splanchnic mesoderm or intermediate mesoderm; together with other organs, the viscus constitutes the respiratory, gastrointestinal, urinary, reproductive and immune systems, or is the central organ of the cardiovascular system. Examples: heart, lung, esophagus, kidney, ovary, spleen. An internal organ of the body; especially: one (as the heart, liver, or intestine) located in the great cavity of the trunk proper.[AAO] general anatomical term in FMA. Note that we place the MA class here temporarily, although properly systems should be distinguished from organs. AAO:0010386 BTO:0001491 EHDAA:512 EMAPA:16245 FMA:7085 MA:0000019 MESH:D014781 NCIT:C28287 RETIRED_EHDAA2:0002201 UMLS:C0042779 XAO:0003034 visceral organ visceral organ system uberon Organsystem@de splanchnic tissue viscera visceral tissue UBERON:0002075 viscus UBERON:0002075 The organ covering the body that consists of the dermis and epidermis. consider 'integumentary system' for invertebrates MA uses the term skin to refer to what is called here: zone of skin BTO:0001253 CALOHA:TS-0934 EFO:0000962 EHDAA2:0001844 EMAPA:17525 FMA:7163 MESH:D012867 MFMO:0000099 NCIT:C12470 OpenCyc:Mx4rvVjX3ZwpEbGdrcN5Y29ycA UMLS:C1123023 XAO:0000023 galen:Skin entire skin skin organ uberon entire integument integument integumental organ pelt skin UBERON:0002097 skin of body UBERON:0002097 Sensory system responsible for the perception of spatial orientation and auditory stimuli. The sensory system used for balance and hearing.[AAO] AAO:0000631 EMAPA:36002 EMAPA:37985 FMA:78500 TAO:0001138 XAO:0003195 ZFA:0001138 auditory organ system vestibuloauditory system uberon auditory system auditory/vestibular system vestibuloauditory system UBERON:0002105 vestibulo-auditory system UBERON:0002105 An exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. Organ which secretes bile and participates in formation of certain blood proteins.[AAO] relationship type change: differentiates_from endoderm (AAO:0000139) CHANGED TO: develops_from endoderm (UBERON:0000925)[AAO] All vertebrates possess a liver (reference 1); Later in craniate evolution, an anterior gill arch was transformed into jaws, and many new types of feeding subsequently evolved.(...) A liver evolved that, among its many functions, stores considerable energy as glycogen or lipid (reference 2).[well established][VHOG] hepatic An organ sometimes referred to as a liver is found associated with the digestive tract of the primitive chordate Amphioxus. However, this is an enzyme secreting gland, not a metabolic organ, and it is unclear how truly homologous it is to the vertebrate liver. The zebrafish liver differs from the mammalian liver in that the hepatocytes are not clearly organized in cords or lobules and the typical portal triads are not apparent. In addition, the zebrafish liver does not have Kuppfer cells. Furthermore, a clear distinction can be made between the male and female liver in the adult zebrafish. The female hepatocytes are very basophilic (Figure 15c) as a result of the production of vitellogenin (Van der Ven et al. 2003). The liver is found in all vertebrates, and is typically the largest visceral organ. Its form varies considerably in different species, and is largely determined by the shape and arrangement of the surrounding organs. Nonetheless, in most species it is divided into right and left lobes; exceptions to this general rule include snakes, where the shape of the body necessitates a simple cigar-like form. The internal structure of the liver is broadly similar in all vertebrates. secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes[GO]. Only ZFA considers this part_of immune system - we weaken this to an overlaps relation, as in general it's only a subset of cells that have clear immune function. AAO:0010111 BTO:0000759 CALOHA:TS-0564 EFO:0000887 EHDAA2:0000997 EHDAA:2197 EMAPA:16846 EV:0100089 FMA:7197 GAID:288 MA:0000358 MAT:0000097 MESH:D008099 MIAA:0000097 NCIT:C12392 OpenCyc:Mx4rvVimppwpEbGdrcN5Y29ycA TAO:0000123 UMLS:C0023884 VHOG:0000257 XAO:0000133 ZFA:0000123 galen:Liver uberon iecur jecur UBERON:0002107 liver UBERON:0002107 Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong]. The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO] Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] AAO:0010397 BTO:0000651 CALOHA:TS-0942 EFO:0000841 EMAPA:32834 EV:0100072 FMA:7200 GAID:313 MA:0000337 MAT:0000047 MESH:A03.492.411.620 MIAA:0000047 NCIT:C12386 OpenCyc:Mx4rvVjlIJwpEbGdrcN5Y29ycA TAO:0001323 UMLS:C0021852 VHOG:0000055 XAO:0000130 ZFA:0001323 galen:SmallIntestine small bowel small intestine uberon anterior intestine intestinum tenue mid intestine UBERON:0002108 small intestine UBERON:0002108 2 cjm Subdivision of digestive tract that connects the stomach to the large intestine and is where much of the digestion and absorption of food takes place (with the exception of ruminants). The mammalian small intestine is long and coiled and can be differentiated histologically into: duodenum, jejunem, ileum[WP,cjm,Kardong]. ISBN10:0073040584 The terminal region of the mid intestine is comprised of specialized enterocytes that appear to play a role in mucosal immunity. Wallace et al, 2005.[TAO] 2012-08-14 TAO:0001323 TAO ZFIN:curator Intestinal surface area also is increased in amphibians and reptiles by internal folds and occasionally by a few villi. The intestine can be divided into a small intestine and a slightly wider large intestine.[well established][VHOG] 2012-09-17 VHOG:0000055 VHOG ISBN:978-0030223693 Liem KF, Bemis WE, Walker WF, Grande L, Functional Anatomy of the Vertebrates: An Evolutionary Perspective (2001) p.566 UMLS:C0021852 ncithesaurus:Small_Intestine intestinum tenue intestinum tenue BTO:0000651 The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one). The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] duodenal In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum. In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz. AAO:0010402 BTO:0000365 CALOHA:TS-0214 EFO:0000851 EMAPA:18852 EV:0100073 FMA:7206 GAID:284 MA:0000338 MAT:0000044 MESH:A03.492.411.620.270 MIAA:0000044 NCIT:C12263 OpenCyc:Mx4rv4LJDpwpEbGdrcN5Y29ycA UMLS:C0013303 VHOG:0000052 XAO:0000236 galen:Duodenum uberon proximal intestine upper intestine UBERON:0002114 duodenum UBERON:0002114 3 cjm The first part of the small intestine. At the junction of the stomach and the duodenum the alimentary canal is inflected. The duodenum first goes anteriorly for a short distance, turns dorsally, and eventually caudally, thus it is a U-shaped structure with two horizontal sections (a ventral and a dorsal one). ISBN:0815318960 The fixed portion of the small intestine deeply lodged in the posterior wall of the abdomen and extending from the pylorus to the beginning of the jejunum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000052 VHOG In fish, the divisions of the small intestine are not as clear, and the terms anterior intestine or proximal intestine may be used instead of duodenum. NCBITaxon:32443 In humans, the duodenum is a hollow jointed tube about 10-15 inches (25-38 centimetres) long connecting the stomach to the jejunum. It begins with the duodenal bulb and ends at the ligament of Treitz. NCBITaxon:9606 UMLS:C0013303 ncithesaurus:Duodenum proximal intestine BTO:0000365 upper intestine BTO:0000365 the portion of the small intestine that extends from the duodenum to the ileum TODO consider ZFA:0001323 mid intestine, see also small intestine The first two fifth of the small intestine beyond the duodenum. It extends from the end of the duodenum to the ileum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] jejunal The jejunum is the middle section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms middle intestine or mid-gut may be used instead of jejunum.[Wikipedia:Jejunum] BTO:0000657 CALOHA:TS-0496 EFO:0001333 EMAPA:18666 EV:0100074 FMA:7207 GAID:318 MA:0000340 MAT:0000045 MESH:A03.492.411.620.625 MIAA:0000045 NCIT:C12388 OpenCyc:Mx4rwATkPJwpEbGdrcN5Y29ycA UMLS:C0022378 VHOG:0000053 galen:Jejunum uberon intestinum jejunum mid-intestine middle intestine UBERON:0002115 jejunum UBERON:0002115 3 cjm the portion of the small intestine that extends from the duodenum to the ileum MGI:monikat MP:0004002 The first two fifth of the small intestine beyond the duodenum. It extends from the end of the duodenum to the ileum. [Dorian_AF, Elsevier's_encyclopaedic_dictionary_of_medicine, Part_B:_Anatomy_(1988)_Amsterdam_etc.:_Elsevier][VHOG] 2012-09-17 VHOG:0000053 VHOG UMLS:C0022378 ncithesaurus:Jejunum intestinum jejunum BTO:0000657 mid-intestine middle intestine BTO:0000657 the portion of the small intestine that extends from the jejunum to the colon TODO consider ZFA:0000706 posterior intestine, see also colon Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] ileal The ileum is the final section of the small intestine in most higher vertebrates, including mammals, reptiles, and birds. In fish, the divisions of the small intestine are not as clear and the terms posterior intestine or distal intestine may be used instead of ileum.[Wikipedia:Ileum] AAO:0010403 BTO:0000620 CALOHA:TS-0472 EFO:0001334 EMAPA:32764 EV:0100075 FMA:7208 GAID:315 MA:0000339 MAT:0000282 MESH:A03.492.411.620.484 MIAA:0000282 NCIT:C12387 OpenCyc:Mx4rvdcLHZwpEbGdrcN5Y29ycA UMLS:C0020885 VHOG:0000647 XAO:0000237 galen:Ileum uberon distal intestine intestinum ileum lower intestine posterior intestine UBERON:0002116 ileum UBERON:0002116 3 cjm the portion of the small intestine that extends from the jejunum to the colon ISBN:0-683-40008-8 MGI:csmith MP:0002581 Although all vertebrates have a digestive tract and accessory glands, various parts of this system are not necessarily homologous, analogous, or even present in all species. Therefore, broad comparisons can be best made under the listings of headgut, foregut, midgut, pancreas and biliary system, hindgut.[uncertain][VHOG] 2012-09-17 VHOG:0000647 VHOG ISBN:978-0521617147 Stevens CE and Hume ID, Comparative physiology of the vertebrate digestive system (2004) p.11 UMLS:C0020885 ncithesaurus:Ileum distal intestine BTO:0000620 intestinum ileum BTO:0000620 lower intestine BTO:0000620 posterior intestine Lung which consists of the right upper lobe, middle lobe and right lower lobe.[FMA] Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0001730 EHDAA:4969 EMAPA:17661 FMA:7309 MA:0000426 NCIT:C33483 OpenCyc:Mx8Ngh4rvgHsHZwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA UMLS:C0225706 VHOG:0000301 uberon UBERON:0002167 right lung UBERON:0002167 Lung which consists of the left upper lobe and left lower lobe.[FMA] Lungs had already developed as paired ventral pockets from the intestine in the ancestor of Osteognathostomata.[well established][VHOG] https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern EHDAA2:0000943 EHDAA:4947 EMAPA:17653 FMA:7310 MA:0000425 NCIT:C32967 OpenCyc:Mx8Ngh4rvgIFoJwpEbGdrcN5Y29ycB4rvVjKy5wpEbGdrcN5Y29ycA UMLS:C0225730 VHOG:0000618 uberon UBERON:0002168 left lung UBERON:0002168 Anatomical cluster consisting of the hematopoietic system and the lymphoid system, or its analogs. CALOHA:TS-2018 EHDAA2:0004615 EMAPA:18765 FMA:74562 MA:0000013 hematolymphoid system lymphomyeloid complex uberon haemolymphoid system UBERON:0002193 hemolymphoid system UBERON:0002193 Anatomical system that consists of the muscular and skeletal systems. Anatomical system that provides locomotion and physical support to the organism.[AAO] There are more than 50,000 extant vertebrate species, representing over 500 million years of evolution. During that time, the vertebrate musculoskeletal systems have adapted to aquatic, terrestrial, fossorial, and arboreal lifestyles, while simultaneously retaining functionally integrated axial and appendicular skeletal systems.[well established][VHOG] musculoskeletal AAO:0010546 CALOHA:TS-1311 EMAPA:32714 EV:0100139 FMA:7482 GAID:98 MA:0002418 MESH:D009141 NCIT:C12754 OpenCyc:Mx4rQRpVNgAKEdyHxgDggVfs8g UMLS:C0026860 VHOG:0001275 VSAO:0000031 XAO:0000168 musculo-skeletal system uberon UBERON:0002204 musculoskeletal system UBERON:0002204 An organ that houses olfactory neurons and is responsible for the sense of smell. Examples include the vertebrate nose and the Drosophila dorsal organ. An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint fma general anatomical term. xao has no subtypes (but Johnstons organ develops from this). An olfactory organ overlaps with the olfactory system, because some parts of the nose (e.g. nasal skeleton) are parts of the skeletal system, which is spatially disjoint AAO:0010180 BTO:0001772 FBbt:00005158 FMA:77659 VHOG:0000287 XAO:0000273 olfactory organ olfactory sense organ olfactory sensory organ main olfactory organ primary olfactory organ uberon olfactory neuroepithelium organ olfactus organum olfactorium UBERON:0002268 olfactory organ UBERON:0002268 Anatomical system that consists of the glands and parts of glands that produce exocrine secretions and help to integrate and control bodily metabolic activity. Exocrine glands are glands that secrete their products (hormones) into ducts (duct glands). They are the counterparts to endocrine glands, which secrete their products (hormones) directly into the bloodstream (ductless glands) or release hormones (paracrines) that affect only target cells nearby the release site. [Wikipedia]. CALOHA:TS-2057 EHDAA2:0002225 EMAPA:35329 FMA:85539 MA:0002411 NCIT:C12957 UMLS:C1516995 WikipediaCategory:Exocrine_system exocrine glandular system uberon UBERON:0002330 exocrine system UBERON:0002330 A gland that secretes products (excluding hormones and other chemical messengers) into ducts (duct glands) which lead directly into the external environment[WP]. Typical exocrine glands include sweat glands, salivary glands, mammary glands, stomach, liver, pancreas Currently this is logically defined by the system it belongs to, but a better system may be base this on presence/absence of ducts. However, the dual nature of the liver should be taken into consideration here. Consider adding subclasses AEO:0000097 BTO:0000765 CALOHA:TS-2012 EHDAA2:0003097 EMAPA:35327 FMA:9596 GAID:34 MA:0002564 MESH:D005088 NCIT:C12712 UMLS:C0015282 ducted gland glandula exocrina uberon UBERON:0002365 exocrine gland UBERON:0002365 Endocrine glands are glands of the endocrine system that secrete their products directly into the circulatory system rather than through a duct.[WP, modified]. AEO:0000098 BTO:0001488 CALOHA:TS-1300 EHDAA2:0003098 EMAPA:35999 FMA:9602 GAID:335 MA:0002563 MESH:D004702 NCIT:C12704 OpenCyc:Mx4rvbkiRZwpEbGdrcN5Y29ycA UMLS:C0014133 ductless gland glandula endocrina uberon ductless gland glandulae endocrinae UBERON:0002368 endocrine gland UBERON:0002368 Anatomical system that is involved in the production of hematopoietic cells. Anatomical system that consists of the blood and blood forming tissues.[AAO] Zebrafish developmental hematopoiesis shows close correspondence to the development of the mammalian hematopoietic system and is regulated by conserved molecular pathways.[well established][VHOG] hematopoietic In humans this is primarily the bone marrow, spleen, tonsils, and lymph nodes AAO:0011002 BTO:0000570 CALOHA:TS-0449 EFO:0000798 EMAPA:35402 EV:0100045 FMA:9667 GAID:1008 MA:0002434 MAT:0000022 MESH:D006413 MIAA:0000022 NCIT:C12909 TAO:0005023 UMLS:C0018957 VHOG:0001624 XAO:0000122 ZFA:0005023 haematological system haemopoietic system organa haemopoietica uberon Blutbildungssystem haematopoietic system hematological system hematolymphoid system hemopoietic system UBERON:0002390 hematopoietic system UBERON:0002390 Lymph is the fluid that is formed when interstitial fluid enters the conduits of the lymphatic system through lymph capillaries[WP]. BTO:0000855 CALOHA:TS-0580 EFO:0000871 ENVO:02000041 EV:0100049 FMA:9671 GAID:1186 MA:0002520 MAT:0000055 MESH:A12.207.630 MIAA:0000055 NCIT:C13252 OpenCyc:Mx4rvpDOU5wpEbGdrcN5Y29ycA UMLS:C0024202 VHOG:0001590 ZFA:0005658 galen:Lymph uberon lympha UBERON:0002391 lymph UBERON:0002391 Anatomical system that protects the body from foreign substances, cells, and tissues by producing the immune response and that includes especially the thymus, spleen, lymphoid tissue, lymphocytes including the B cells and T cells, and antibodies. The antibody-based immune system defined by the presence of the major histocompatibility complex (MHC), T cell receptor (TCR), B cell receptor (BCR) or recombination activating genes (RAGs) is known beginning from jawed fishes.[well established][VHOG] AAO:0011003 BILA:0000104 BTO:0005810 FMA:9825 GAID:328 MA:0002711 MESH:D007107 NCIT:C12735 OpenCyc:Mx4rvWNkm5wpEbGdrcN5Y29ycA TAO:0001159 UMLS:C0020962 VHOG:0001247 XAO:0003152 ZFA:0001159 uberon UBERON:0002405 immune system UBERON:0002405 Connected anatomical system that forms a barrier between an animal and its environment. In vertebrates, the integumental system consists of the epidermis, dermis plus associated glands and adnexa such as hair and scales. In invertebrates, the integumental system may include cuticle. (...) the integument of many tetrapods is reinforced by a morphologically and structurally diverse assemblage of skeletal elements. These elements are widely understood to be derivatives of the once all-encompassing dermal skeleton of stem-gnathostomes (...).[well established][VHOG] UBERON:0007029 AEO:0000154 BILA:0000118 CALOHA:TS-1299 CARO:0002001 EFO:0000807 EHDAA2:0000836 EHDAA2_RETIRED:0003154 EHDAA:6520 EMAPA:17524 EV:0100151 FBbt:00004969 FMA:72979 HAO:0000421 MA:0000014 MAT:0000033 MESH:D034582 MIAA:0000033 NCIT:C12907 TADS:0000108 UMLS:C0037267 VHOG:0000403 XAO:0000176 galen:Surface integumentary system uberon body surface dermal system external covering of organism integumentum commune organism surface surface UBERON:0002416 integumental system UBERON:0002416 The lymphatic system in vertebrates is a network of conduits that carry a clear fluid called lymph. It also includes the lymphoid tissue through which the lymph travels. Lymphoid tissue is found in many organs, particularly the lymph nodes, and in the lymphoid follicles associated with the digestive system such as the tonsils. The system also includes all the structures dedicated to the circulation and production of lymphocytes, which includes the spleen, thymus, bone marrow and the lymphoid tissue associated with the digestive system[WP]. Part of the circulatory system which consists of a series of vessels which collect blood (exclusive of erythrocytes) which seep through capillary walls and return it to the veins.[AAO] Tetrapods have evolved distinct lymphatic systems, in which lymphatic capillaries help drain most of the tissues of the body.[well established][VHOG] lymphoid The lymphatic system of anuran amphibians is characterized by large lymphatic sacs and two pairs of lymph hearts that return lymph into the venous circulation but no lymph vessels per se [10.1152/japplphysiol.00201.2013] The lymphatic systems of reptiles and some birds have lymph hearts, and both groups have extensive lymph vessels, but their functional role in both lymph movement and plasma volume homeostasis is almost completely unknown [10.1152/japplphysiol.00201.2013] We follow FMA and MA in distinguishing between lymphatic system and lymphoid system, with lymhoid tissue part of the non-lymphatic component, although these terms are often used interchangeably. We assume the ZFA term lymphatic tissue actually corresponds to the broader class (e.g. ZFA lymph node in the ZFA lymphatic system). See tracker for more comments. UBERON:0002096 EHDAA2:0001043 EHDAA:8677 EMAPA:37664 FMA:74594 GAID:931 MA:0002435 MAT:0000197 MIAA:0000197 NCIT:C12746 OpenCyc:Mx4rwQAKT5wpEbGdrcN5Y29ycA TAO:0000385 UMLS:C0024235 VHOG:0000842 XAO:0003199 ZFA:0000385 lymphatic system uberon lymphatic circulatory system lymphatic drainage system systema lymphoideum UBERON:0002465 lymphoid system UBERON:0002465 an organ that functions as a secretory or excretory organ glandular UBERON:MIAA_0000021 AAO:0000212 AEO:0000096 BTO:0000522 EFO:0000797 EHDAA2:0003096 EHDAA:2161 EHDAA:4475 EHDAA:6522 EMAPA:18425 FBbt:00100317 FMA:7146 FMA:86294 HAO:0000375 MA:0003038 MAT:0000021 MIAA:0000021 NCIT:C13319 OpenCyc:Mx4rwP3vyJwpEbGdrcN5Y29ycA UMLS:C1285092 WikipediaCategory:Glands galen:Gland glandular organ uberon Druese glandula UBERON:0002530 gland UBERON:0002530 Anatomical structure that has as its parts two or more multi-tissue structures of at least two different types and which through specific morphogenetic processes forms a single distinct structural unit demarcated by bona fide boundaries from other distinct anatomical structures of different types. this class was introduced for consistency with CARO. However, in this ontology we typically classify organs directly under 'organ' rather than subdividing into compound and simple organs AAO:0010015 AEO:0000024 BILA:0000024 CARO:0000024 EHDAA2:0003024 HAO:0000024 TADS:0000598 TAO:0000496 TGMA:0001837 VHOG:0001723 XAO:0003041 ZFA:0000496 uberon organ UBERON:0003103 compound organ UBERON:0003103 An organ involved in reproduction GO uses genitalia for the singular organ EMAPA:17381 EMAPA:37731 MA:0001752 MESH:D005835 NCIT:C25177 OpenCyc:Mx4rwO39aJwpEbGdrcN5Y29ycA TGMA:0000591 UMLS:C0017420 WBbt:0008422 genital organ reproductive system organ sex organ uberon genitalia UBERON:0003133 reproductive organ UBERON:0003133 A gland that is part of a foregut [Automatically generated definition]. EHDAA2:0000567 EHDAA:950 EMAPA:16557 VHOG:0000650 foregut gland uberon UBERON:0003294 gland of foregut UBERON:0003294 A gland that is part of a integumental system [Automatically generated definition]. EHDAA2:0000837 EHDAA:6522 EMAPA:17758 MA:0000144 VHOG:0000654 integumental gland integumental system gland integumentary gland uberon UBERON:0003297 gland of integumental system UBERON:0003297 A gland that is part of a digestive tract [Automatically generated definition]. EMAPA:18815 MA:0003202 digestive tract gland gland of digestive tract gland of lower gastrointestinal tract gut gland lower gastrointestinal tract gland uberon UBERON:0003408 gland of digestive tract UBERON:0003408 Any tube, opening or passage that connects two distinct anatomical spaces. FMA has both conduit and conduit space. In EHDAA2 this is a surface feature AEO:0000080 EHDAA2:0003080 FMA:242873 foramen foramina uberon opening ostia ostium UBERON:0004111 anatomical conduit UBERON:0004111 An anatomical structure that develops (entirely or partially) from the endoderm. Grouping term for query purposes uberon UBERON:0004119 endoderm-derived structure UBERON:0004119 An anatomical structure that develops (entirely or partially) from the mesoderm. Grouping term for query purposes FBbt:00025998 mesodermal derivative uberon UBERON:0004120 mesoderm-derived structure UBERON:0004120 An anatomical structure that develops (entirely or partially) from the ectoderm. Grouping term for query purposes FBbt:00025990 ectodermal deriviative uberon UBERON:0004121 ectoderm-derived structure UBERON:0004121 Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction. Anatomical system that has as its parts the organs concerned with the production and excretion of urine and those concerned with reproduction.[AAO] relationship type change: differentiates_from intermediate mesoderm (AAO:0010575) CHANGED TO: develops_from intermediate mesoderm (UBERON:0003064)[AAO] Kidneys and gonads (of vertebrates) develop from adjacent tissues, and after the excretory or urinary ducts have developed, the reproductive system usually taps into them or their derivatives.[well established][VHOG] genitourinary urogenital AAO:0000624 BILA:0000122 BTO:0003091 EFO:0003864 EHDAA:1013 EMAPA:16367 EV:0100094 FMA:280610 GAID:362 MESH:D014566 NCIT:C12810 OpenCyc:Mx4rQRpVMgAKEdyHxgDggVfs8g UMLS:C0042066 VHOG:0000286 XAO:0000140 galen:GenitoUrinarySystem urogenital system uberon GU tract UG tract Urogenitalsystem genito-urinary system genitourinary tract urogenital tract UBERON:0004122 genitourinary system UBERON:0004122 The external genitalia are the outer sex organs, such as the penis or vulva in mammals FMA:45643 external genitalia uberon external reproductive organ external sex organ UBERON:0004176 TODO: make a subdivision of reproductive system. Relabel. See https://github.com/obophenotype/uberon/issues/547 external genitalia UBERON:0004176 Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body. Anatomical cluster that consists of all the skeletal elements (eg., bone, cartilage, and teeth) of the body.[VSAO] skeletal AEO:0000168 EHDAA2:0001843 EHDAA:5047 EMAPA:17213 FMA:23875 GAID:177 MA:0003006 MAT:0000032 MESH:D012863 MIAA:0000032 OpenCyc:Mx4rvVi1rpwpEbGdrcN5Y29ycA VSAO:0000026 XAO:0004053 galen:Skeleton set of all bones set of bones of body uberon UBERON:0004288 skeleton https://github.com/obophenotype/uberon/wiki/The-skeletal-system UBERON:0004288 Sum of all sensory systems in an organism. note the distinct between entire sensory system and individual system. this reconciles is_a and part_of distinctions between ssAOs FMA:78499 sense organ system uberon UBERON:0004456 entire sense organ system UBERON:0004456 Anatomical system that has as its parts the heart and blood vessels. we treat cardiovascular as part of circulatory system, with the latter including other kinds of circulation, including lymph. The vessels of the cardiovascular system are as varied as the diverse organs they supply. However, these variations are based on modifications of a fundamental plan of organization common to vertebrates.[well established][VHOG] AAO:0011001 BILA:0000016 BTO:0000088 CALOHA:TS-1297 EFO:0000791 EHDAA2:0000216 EHDAA:394 EMAPA:16104 EMAPA:16370 EV:0100017 FMA:7161 GAID:467 MA:0000010 MAT:0000016 MESH:D002319 MIAA:0000016 NCIT:C12686 OpenCyc:Mx4rvVjzG5wpEbGdrcN5Y29ycA TAO:0000010 UMLS:C0007226 VHOG:0000302 WikipediaCategory:Cardiovascular_system XAO:0000100 XAO:0001010 ZFA:0000010 uberon CV system Herz und Gefaesssystem UBERON:0004535 cardiovascular system UBERON:0004535 The part of the cardiovascular system consisting of all arteries. The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] BTO:0004690 EHDAA2:0000143 EHDAA:396 EMAPA:16201 EMAPA:16371 MA:0002719 VHOG:0000273 uberon UBERON:0004572 arterial system UBERON:0004572 The part of the cardiovascular system consisting of all venous vessels. In vertebrates with a double circulation, this can be divided into systemic and pulmonary portions. The appearance of Chordata and subsequently the vertebrates is accompanied by a rapid structural diversification of this primitive linear heart: looping, unidirectional circulation, an enclosed vasculature, and the conduction system.[well established][VHOG] BTO:0004692 EHDAA2:0002171 EHDAA:486 EMAPA:16240 MA:0002720 NCIT:C33858 UMLS:C1267406 VHOG:0000277 vein system uberon UBERON:0004582 venous system UBERON:0004582 Organ consisting of skeletal tissue. Encompasses whole bones, fused bones, cartilaginious elements, teeth, dermal denticles. Organ entity that is typically involved in mechanical support and may have different skeletal tissue compositions at different stages.[VSAO] Organ entity that may have different tissue compositions at different stages and is typically involved in mechanical support.[TAO] AAO:0011129 TAO:0001890 VSAO:0000128 XAO:0004012 ZFA:0005494 galen:SkeletalStructure uberon UBERON:0004765 skeletal element UBERON:0004765 Anatomical system that consists of all the joints of the body. EMAPA:35150 FMA:23878 MA:0003007 VSAO:0000181 joint system set of all joints of body uberon set of all joints set of joints of body UBERON:0004770 articular system UBERON:0004770 A proximal-distal subdivision of the digestive tract. intended to denote both embryonic and adult structures. Note the FMA grouping here is not quite correct. FBbt:00100315 FMA:71131 uberon alimentary system subdivision intestinal tract segment of intestinal tract subdivision of alimentary system UBERON:0004921 subdivision of digestive tract UBERON:0004921 A proximal-distal subdivision of the digestive tract. alimentary system subdivision FMA:71131 subdivision of alimentary system FMA:71131 An organ that is part of a immune system [Automatically generated definition]. immune system organ uberon UBERON:0005057 immune organ UBERON:0005057 Any anatomical structure that is part of the reproductive system. reproductive system element reproductive system structure uberon UBERON:0005156 reproductive structure UBERON:0005156 An organ or element that is in the abdomen. Examples: spleen, intestine, kidney, abdominal mammary gland. MA:0000522 abdomen organ uberon UBERON:0005172 abdomen element UBERON:0005172 An organ or element that is part of the adbominal segment of the organism. This region can be further subdivided into the abdominal cavity and the pelvic region. EMAPA:37062 MA:0000529 abdominal segment organ uberon UBERON:0005173 abdominal segment element UBERON:0005173 An organ or element that part of the dorsum of the organism. Examples: spinal cord, vertebrae, muscles of back. EMAPA:37274 MA:0001901 back organ dorsal region organ uberon UBERON:0005174 dorsal region element UBERON:0005174 An organ or element that part of the trunk region. The trunk region can be further subdividied into thoracic (including chest and thoracic cavity) and abdominal (including abdomen and pelbis) regions. EMAPA:37270 MA:0000516 trunk organ uberon UBERON:0005177 trunk region element UBERON:0005177 An organ or element that is in the thoracic cavity. Examples: lung, heart, longus colli. EMAPA:37273 MA:0000557 thoracic cavity organ uberon UBERON:0005178 thoracic cavity element UBERON:0005178 An organ that part of the thoracic segment region. This region can be further subdividied chest and thoracic cavity regions. EMAPA:37271 MA:0000563 uberon upper body organ UBERON:0005181 thoracic segment organ UBERON:0005181 The part of the digestive system that excludes the hepatobiliary system. the decision to split digestive and gastrointestinal in this way may be revisited. As it currently stands, this class more closely aligns what MA calls the alimentary system The system that includes the esophagus, stomach, small and large intestine, anus, liver, biliary tract, and pancreas[ncithesaurus:Gastrointestinal_System]. All metazoans (with degenerate exceptions) have some sort of digestive cavity with a means of entrance to and exit from it.[well established][VHOG] that many anatomy ontologies consider this synonymous with digestive system. here we follow MA in dividing digestive system into gastrointestinal and hepatobiliary. hepatobiliary includes the liver and biliary tract. species-specific AO classes are categorized according to whether liver is included. For example, XAO includes liver as part of XAO:0000125 alimentary system, so we assume this class is the more generic class. We have one entity that is part of both gastrointestinal and hepatobiliary systems: hepatopancreatic ampulla. BTO:0000058 CALOHA:TS-0407 EHDAA2:0000110 EHDAA:514 EMAPA:16246 EV:0100056 FMA:71132 GAID:294 MA:0000323 MESH:A03.492 NCIT:C12378 UMLS:C0012240 VHOG:0000412 galen:GastrointestinalTract uberon GI tract alimentary system alimentary tract gastro-intestinal system gastroenterological system gastrointestinal (GI) tract gastrointestinal system gastrointestinal tract UBERON:0005409 alimentary part of gastrointestinal system UBERON:0005409 AEO:0000125 CALOHA:TS-2122 EHDAA2:0003125 FBbt:00007006 FMA:292313 MIAA:0000019 uberon developing structure developmental structure developmental tissue UBERON:0005423 developing anatomical structure UBERON:0005423 A acellular anatomical structure that is the bounding layer of a anatomical structure. FMA:63871 uberon UBERON:0005764 acellular membrane UBERON:0005764 An acellular membrane that is part of the epithelium, lies adjacent to the epithelial cells, and is the fusion of the the basal lamina and the reticular lamina. this class represents a continuous sheet of basement membrane which can underlie multiple epithelial cells over large regions. In contrast, the GO class 'basal membrane' represents a portion of substance on the scale of a single cell. AAO:0010596 FMA:63872 GAID:915 NCIT:C13191 UMLS:C0004799 basement membrane of connective tissue membrana basalis uberon basement membrane UBERON:0005769 basement membrane of epithelium UBERON:0005769 Liquid components of living organisms. includes fluids that are excreted or secreted from the body as well as body water that normally is not. fluid EMAPA:37441 FMA:280556 GAID:266 MESH:D001826 galen:BodyFluid body fluid uberon UBERON:0006314 bodily fluid UBERON:0006314 A substance that is secreted by a mammary gland. The substance may differ depending on phase, with colostrum produced during pregancy/early lactation, and milk produced afterwards. EMAPA:36538 MA:0002505 uberon lactiferous gland fluid lactiferous gland secretion mammary gland fluid mammary gland secreted fluid mammary gland secretion secretion of mammary gland UBERON:0006539 mammary gland fluid/secretion UBERON:0006539 The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. currently this is an extremely generic class, encompassing both protostomes and deuterostomes. branchial pharyngeal FBbt:00005380 MAT:0000049 MIAA:0000049 uberon anterior part of foregut pharyngeal tube UBERON:0006562 pharynx UBERON:0006562 The pharynx is the part of the digestive system immediately posterior to the mouth[GO]. GO:0060465 Any gland that is part of the digestive system. AAO:0000130 BTO:0000345 uberon digestive gland UBERON:0006925 digestive system gland UBERON:0006925 A hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood or analogs[GO,modified]. note we reserve the subclass 'heart' from the vertebrate multi-chambered heart. 'The first heart-like organ is believed to have appeared 500my ago in an ancestral bilaterian'. Amniotes: four-chambered heart. Amphibians: two atria, one ventricle, pulmonary; fish: single atrium and ventricle; amphioxus: tubular, non-striated, closed, unidirectional; ascidians: tubular, striated, open, bidirectional; arthropods: tubular, open; C elegans: contractile pharynx; Cnideria: striated muscle cells associated with gastrodermis FBbt:00003154 SPD:0000130 TADS:0000147 dorsal tube heart uberon adult heart UBERON:0007100 Gene notes: Bmp, Nkx, Gata primary circulatory organ UBERON:0007100 The first chamber in the alimentary canal of a ruminant stomach, composed of the rumen and reticulum. retriculo-rumen uberon UBERON:0007364 reticulorumen UBERON:0007364 The first chamber in the alimentary canal of a ruminant stomach, composed of the rumen and reticulum. The hard-shelled reproductive body produced by a bird and especially by the common domestic chicken; also: its contents used as food. BSA:0000081 BTO:0000369 uberon egg UBERON:0007379 shelled egg UBERON:0007379 Any bodily fluid that has passed through a membrane such as the capillary wall, as a result of unbalanced hydrostatic and osmotic forces transudative characteristically low in protein and cellular content (unless there has been secondary concentration) FMA:12276 GAID:1195 MESH:D005122 ncithesaurus:Transudate uberon plasma ultrafiltrate UBERON:0007779 transudate UBERON:0007779 Any fluid produced by a serous gland. serous fluid serosal fluid serous gland fluid uberon UBERON:0007794 secretion of serous gland UBERON:0007794 Anatomical system that consists of all blood and lymph vessels. consider merging with vasculature The cardiovascular and lymphatic systems, collectively[ncithesaurus:Vascular_System]. in both MA and BTO, the arterial system and venous sytem are subtypes of the vascular system BTO:0001085 CALOHA:TS-2053 EHDAA2:0004520 EMAPA:35905 MA:0002718 NCIT:C33854 UMLS:C0489903 uberon Gefaesssystem@de UBERON:0007798 vascular system UBERON:0007798 The gastric glands in the pyloric region of the stomach; the pyloric glands secrete mucin, which coats the stomach and protects it, and hormones such as gastrin and enkephalin[MP]. check relationship to pylorus vs antrum EMAPA:27211 FMA:14922 NCIT:C33431 UMLS:C0227239 glandula pylorica pyloric antrum gland pyloric gland pyloric mucuous gland uberon UBERON:0008861 pyloric gastric gland UBERON:0008861 EHDAA2:0001371 uberon pancreatis dorsalis UBERON:0009708 dorsal pancreas UBERON:0009708 EHDAA2:0001393 uberon pancreatis ventralis UBERON:0009709 ventral pancreas UBERON:0009709 Branch or outpocketing of the digestive tract. FBbt:00100316 uberon diverticulum of gut intestinal pouch UBERON:0009854 digestive tract diverticulum UBERON:0009854 Branch or outpocketing of the digestive tract. diverticulum of gut FBbt:00100316 galen:Diverticulum pouch uberon diverticulum UBERON:0009856 sac UBERON:0009856 An anatomical structure that has more than one cell as a part. CARO:0010000 FBbt:00100313 multicellular structure uberon UBERON:0010000 multicellular anatomical structure UBERON:0010000 An organ of the digestive tract that is capable of retaining and storing food This is a very broad functionally defined grouping class that collects disparate structures from insects to vertebrates BSA:0000123 TADS:0000172 TGMA:0001041 uberon UBERON:0010039 food storage organ UBERON:0010039 the FMA class specifically refers to ureter FMA:63212 MESH:D024022 NCIT:C32339 NIF_Subcellular:sao7547390221 uberon UBERON:0011860 collection of collagen fibrils UBERON:0011860 A blood that is part of a vein. FMA:83067 blood in vein portion of venous blood venous blood uberon UBERON:0013756 venous blood UBERON:0013756 Any of the organs or elements that are part of the digestive system. Examples: tongue, esophagus, spleen, crop, lunge feeding organ, tooth elements. EMAPA:37843 digestive organ digestive system organ uberon UBERON:0013765 digestive system element UBERON:0013765 Any structure that is placed on one side of the left-right axis of a bilaterian. This class is primarily to implement taxon constraints. It may be removed in the future. uberon UBERON:0015212 lateral structure UBERON:0015212 A hollow, muscular organ, which, by contracting rhythmically, contributes to the circulation of lymph, blood or analogs. Examples: a chambered vertebrate heart; the tubular peristaltic heart of ascidians; the dorsal vessel of an insect; the lymoh heart of a reptile. heart SPD:0000130 cardiac pump heart or heart like organ circulatory vessel uberon cardiac structure UBERON:0015228 circulatory organ UBERON:0015228 EMAPA:37597 MA:0002449 heart/pericardium uberon UBERON:0015410 heart plus pericardium UBERON:0015410 A viscus that is part of a abdomen. FMA:32413 FMA:67355 abdominal viscera abdominal viscera set set of abdominal viscera uberon UBERON:0017672 abdominal viscera UBERON:0017672 An exocrine gland that is part of a integumental system. integumental exocrine gland integumental system exocrine gland uberon UBERON:0019319 exocrine gland of integumental system UBERON:0019319 Any substance in the body or expelled from the body that is in a gaseous state. FMA:84580 gas in anatomical space portion of gas in anatomical space uberon UBERON:0034873 bodily gas UBERON:0034873 Any portion of gas located in a part of the respiratory system that is composed primarily of air. FMA:84581 respiratory air respiratory system air uberon UBERON:0034874 air in respiratory system UBERON:0034874 An multicellular anatomical structure that has subparts of multiple organs as a part. CARO:0020001 uberon anatomical cluster UBERON:0034921 multi organ part structure UBERON:0034921 A cluster of cells, largely surrounded by a morphological boundary. CARO:0020002 FMA:62807 uberon UBERON:0034922 cell cluster UBERON:0034922 A collection of anatomical structures that are alike in terms of their morphology or developmental origin. resolve if this should be a subclass of disconnected anatomical group. Some collections (e.g. the skeleton or skull) are arguably connected uberon UBERON:0034925 anatomical collection UBERON:0034925 Any portion of gas located in a part of the respiratory system. respiratory gas respiratory system gas uberon UBERON:0034947 gas in respiratory system UBERON:0034947 waiting:placement awaiting ontology review/placement a geopolitical region is a geographic region recognized by social or legal convention. geopolitical region A township is a rural or sub-urban settlement. township owl:Thing 1つのエージェントによって公開またはキュレートされ、1つ以上の形式でアクセスまたはダウンロードできるデータの集合。 A collection of data, published or curated by a single source, and available for access or download in one or more represenations. Kolekce dat poskytovaná či řízená jedním zdrojem, která je k dispozici pro přístup či stažení v jednom či více formátech. Raccolta di dati, pubblicati o curati da un'unica fonte, disponibili per l'accesso o il download in uno o più formati. Una colección de datos, publicados o conservados por una única fuente, y disponibles para ser accedidos o descargados en uno o más formatos. Une collection de données, publiée ou élaborée par une seule source, et disponible pour accès ou téléchargement dans un ou plusieurs formats. Μία συλλογή από δεδομένα, δημοσιευμένη ή επιμελημένη από μία και μόνο πηγή, διαθέσιμη δε προς πρόσβαση ή μεταφόρτωση σε μία ή περισσότερες μορφές. قائمة بيانات منشورة أو مجموعة من قبل مصدر ما و متاح الوصول إليها أو تحميلها Conjunto de datos Dataset Dataset Datová sada Jeu de données Σύνολο Δεδομένων قائمة بيانات データセット 2018-02 - odstraněno tvrzení o podtřídě dctype:Dataset, jelikož rozsah dcat:Dataset zahrnuje několik dalších typů ze slovníku dctype. 2018-02 - se eliminó el axioma de subclase con dctype:Dataset porque el alcance de dcat:Dataset incluye muchos otros tipos del vocabulario dctype. 2018-02 - sottoclasse di dctype:Dataset rimosso perché l'ambito di dcat:Dataset include diversi altri tipi dal vocabolario dctype. 2018-02 - subclass of dctype:Dataset removed because scope of dcat:Dataset includes several other types from the dctype vocabulary. 1つのエージェントによって公開またはキュレートされ、1つ以上の形式でアクセスまたはダウンロードできるデータの集合。 A collection of data, published or curated by a single source, and available for access or download in one or more represenations. Kolekce dat poskytovaná či řízená jedním zdrojem, která je k dispozici pro přístup či stažení v jednom či více formátech. Raccolta di dati, pubblicati o curati da un'unica fonte, disponibili per l'accesso o il download in uno o più formati. Una colección de datos, publicados o conservados por una única fuente, y disponibles para ser accedidos o descargados en uno o más formatos. Une collection de données, publiée ou élaborée par une seule source, et disponible pour accès ou téléchargement dans un ou plusieurs formats. Μία συλλογή από δεδομένα, δημοσιευμένη ή επιμελημένη από μία και μόνο πηγή, διαθέσιμη δε προς πρόσβαση ή μεταφόρτωση σε μία ή περισσότερες μορφές. قائمة بيانات منشورة أو مجموعة من قبل مصدر ما و متاح الوصول إليها أو تحميلها Cette classe représente le jeu de données publié par le fournisseur de données. Dans les cas où une distinction est nécessaire entre le jeu de donénes et son entrée dans le catalogue, la classe registre de données peut être utilisée pour ce dernier. Esta clase representa el conjunto de datos publicados. En los casos donde es necesario distinguir entre el conjunto de datos y su entrada en el catálogo de datos, se debe utilizar la clase 'registro del catálogo'. Questa classe descrive il dataset dal punto di vista concettuale. Possono essere disponibili una o più rappresentazioni, con diversi layout e formati schematici o serializzazioni. Questa classe rappresenta il dataset come pubblicato dall’editore. Nel caso in cui sia necessario operare una distinzione fra i metadati originali del dataset e il record dei metadati ad esso associato nel catalogo (ad esempio, per distinguere la data di modifica del dataset da quella del dataset nel catalogo) si può impiegare la classe catalog record. Tato třída reprezentuje datovou sadu tak, jak je publikována poskytovatelem dat. V případě potřeby rozlišení datové sady a jejího katalogizačního záznamu (jelikož metadata jako datum modifikace se mohou lišit) pro něj může být použita třída "katalogizační záznam". This class describes the conceptual dataset. One or more representations might be available, with differing schematic layouts and formats or serializations. This class represents the actual dataset as published by the dataset provider. In cases where a distinction between the actual dataset and its entry in the catalog is necessary (because metadata such as modification date and maintainer might differ), the catalog record class can be used for the latter. Η κλάση αυτή αναπαριστά το σύνολο δεδομένων αυτό καθ'εαυτό, όπως έχει δημοσιευθεί από τον εκδότη. Σε περιπτώσεις όπου είναι απαραίτητος ο διαχωρισμός μεταξύ του συνόλου δεδομένων και της καταγραφής αυτού στον κατάλογο (γιατί μεταδεδομένα όπως η ημερομηνία αλλαγής και ο συντηρητής μπορεί να διαφέρουν) η κλάση της καταγραφής καταλόγου μπορεί να χρησιμοποιηθεί για το τελευταίο. このクラスは、データセットの公開者が公開する実際のデータセットを表わします。カタログ内の実際のデータセットとそのエントリーとの区別が必要な場合（修正日と維持者などのメタデータが異なるかもしれないので）は、後者にcatalog recordというクラスを使用できます。 hso:HSO_0000057 supra-national geopolitical entity COUNTRY CY Cyprus Republic of Cyprus Cyprus COUNTRY AU Australia Commonwealth of Australia Australia COUNTRY AU Australia Commonwealth of Australia COUNTRY NZ New Zealand New Zealand New Zealand COUNTRY NZ New Zealand New Zealand COUNTRY TR Turkey Republic of Turkey Turkey COUNTRY TR Turkey Republic of Turkey COUNTRY SD Sudan Republic of the Sudan Sudan COUNTRY SD Sudan Republic of the Sudan COUNTRY TN Tunisia Republic of Tunisia Tunisia COUNTRY TN Tunisia Republic of Tunisia COUNTRY DZ Algeria People’s Democratic Republic of Algeria Algeria COUNTRY DZ Algeria People’s Democratic Republic of Algeria COUNTRY MA Morocco Kingdom of Morocco Morocco COUNTRY MA Morocco Kingdom of Morocco COUNTRY LY Libya Libya Libya COUNTRY LY Libya Libya COUNTRY ET Ethiopia Federal Democratic Republic of Ethiopia Ethiopia COUNTRY ET Ethiopia Federal Democratic Republic of Ethiopia COUNTRY ER Eritrea State of Eritrea Eritrea COUNTRY ER Eritrea State of Eritrea COUNTRY DJ Djibouti Republic of Djibouti Djibouti COUNTRY DJ Djibouti Republic of Djibouti COUNTRY MR Mauritania Islamic Republic of Mauritania Mauritania COUNTRY MR Mauritania Islamic Republic of Mauritania COUNTRY ML Mali Republic of Mali Mali COUNTRY ML Mali Republic of Mali COUNTRY NE Niger Republic of Niger Niger COUNTRY NE Niger Republic of Niger COUNTRY TD Chad Republic of Chad Chad COUNTRY TD Chad Republic of Chad COUNTRY ES Spain Kingdom of Spain Spain COUNTRY ES Spain Kingdom of Spain COUNTRY IS Iceland Iceland Iceland COUNTRY IS Iceland Iceland COUNTRY BJ Benin Republic of Benin Benin COUNTRY BJ Benin Republic of Benin COUNTRY BF Burkina Faso Burkina Faso Burkina Faso COUNTRY BF Burkina Faso Burkina Faso COUNTRY CI Côte d’Ivoire Republic of Côte d’Ivoire Cote d'Ivoire COUNTRY CI Côte d’Ivoire Republic of Côte d’Ivoire COUNTRY GM The Gambia Republic of The Gambia Gambia COUNTRY GM The Gambia Republic of The Gambia COUNTRY GH Ghana Republic of Ghana Ghana COUNTRY GH Ghana Republic of Ghana COUNTRY GN Guinea Republic of Guinea Guinea COUNTRY GN Guinea Republic of Guinea COUNTRY GW Guinea-Bissau Republic of Guinea-Bissau Guinea-Bissau COUNTRY GW Guinea-Bissau Republic of Guinea-Bissau COUNTRY LR Liberia Republic of Liberia Liberia COUNTRY LR Liberia Republic of Liberia COUNTRY NG Nigeria Federal Republic of Nigeria Nigeria COUNTRY NG Nigeria Federal Republic of Nigeria COUNTRY SN Senegal Republic of Senegal Senegal COUNTRY SN Senegal Republic of Senegal COUNTRY SL Sierra Leone Republic of Sierra Leone Sierra Leone COUNTRY SL Sierra Leone Republic of Sierra Leone COUNTRY TG Togo Togolese Republic Togo COUNTRY TG Togo Togolese Republic COUNTRY CG Congo Republic of the Congo Democratic Republic of the Congo COUNTRY CG Congo Republic of the Congo COUNTRY RW Rwanda Republic of Rwanda Rwanda COUNTRY RW Rwanda Republic of Rwanda COUNTRY CD Democratic Republic of the Congo Democratic Republic of the Congo Republic of Congo COUNTRY CD Democratic Republic of the Congo Democratic Republic of the Congo COUNTRY BI Burundi Republic of Burundi Burundi COUNTRY BI Burundi Republic of Burundi COUNTRY GQ Equatorial Guinea Republic of Equatorial Guinea Equatorial Guinea COUNTRY GQ Equatorial Guinea Republic of Equatorial Guinea COUNTRY GA Gabon Gabonese Republic Gabon COUNTRY GA Gabon Gabonese Republic COUNTRY CM Cameroon Republic of Cameroon Cameroon COUNTRY CM Cameroon Republic of Cameroon COUNTRY ZA South Africa Republic of South Africa Republic of South Africa COUNTRY ZA South Africa Republic of South Africa COUNTRY AO Angola Republic of Angola Angola COUNTRY AO Angola Republic of Angola COUNTRY NA Namibia Republic of Namibia Namibia COUNTRY NA Namibia Republic of Namibia COUNTRY BW Botswana Republic of Botswana Botswana COUNTRY BW Botswana Republic of Botswana COUNTRY LS Lesotho Kingdom of Lesotho Lesotho COUNTRY LS Lesotho Kingdom of Lesotho COUNTRY SZ Swaziland Kingdom of Swaziland Swaziland COUNTRY SZ Swaziland Kingdom of Swaziland COUNTRY MZ Mozambique Republic of Mozambique Mozambique COUNTRY MZ Mozambique Republic of Mozambique COUNTRY KE Kenya Republic of Kenya Kenya COUNTRY KE Kenya Republic of Kenya COUNTRY UG Uganda Republic of Uganda Uganda COUNTRY UG Uganda Republic of Uganda COUNTRY TZ Tanzania United Republic of Tanzania Tanzania COUNTRY TZ Tanzania United Republic of Tanzania COUNTRY SO Somalia Federal Republic of Somalia Somalia COUNTRY SO Somalia Federal Republic of Somalia COUNTRY MW Malawi Republic of Malawi Malawi COUNTRY MW Malawi Republic of Malawi COUNTRY ZW Zimbabwe Republic of Zimbabwe Zimbabwe COUNTRY ZW Zimbabwe Republic of Zimbabwe COUNTRY ZM Zambia Republic of Zambia Zambia COUNTRY ZM Zambia Republic of Zambia COUNTRY CV Cape Verde Republic of Cape Verde Cape Verde COUNTRY CV Cape Verde Republic of Cape Verde COUNTRY BB Barbados Barbados Barbados COUNTRY BB Barbados Barbados COUNTRY JO Jordan Hashemite Kingdom of Jordan Jordan COUNTRY JO Jordan Hashemite Kingdom of Jordan COUNTRY SY Syria Syrian Arab Republic Syria COUNTRY SY Syria Syrian Arab Republic COUNTRY IL Israel State of Israel Israel COUNTRY IL Israel State of Israel COUNTRY LB Lebanon Lebanese Republic Lebanon COUNTRY LB Lebanon Lebanese Republic COUNTRY BO Bolivia Plurinational State of Bolivia Bolivia COUNTRY BO Bolivia Plurinational State of Bolivia COUNTRY GY Guyana Cooperative Republic of Guyana Guyana COUNTRY GY Guyana Cooperative Republic of Guyana COUNTRY SR Suriname Republic of Suriname Suriname COUNTRY SR Suriname Republic of Suriname COUNTRY CA Canada Canada Canada COUNTRY CA Canada Canada COUNTRY GB United Kingdom United Kingdom of Great Britain and Northern Ireland United Kingdom COUNTRY GB United Kingdom United Kingdom of Great Britain and Northern Ireland Scotland Wales England COUNTRY DE Germany Federal Republic of Germany begin_date: 1990-10-03. Germany COUNTRY DE Germany Federal Republic of Germany COUNTRY IT Italy Italian Republic Italy COUNTRY IT Italy Italian Republic COUNTRY NO Norway Kingdom of Norway Norway COUNTRY NO Norway Kingdom of Norway COUNTRY HR Croatia Republic of Croatia Croatia COUNTRY HR Croatia Republic of Croatia COUNTRY RU Russia Russian Federation begin_date: 1991-12. Russia COUNTRY RU Russia Russian Federation COUNTRY UA Ukraine Ukraine Ukraine COUNTRY UA Ukraine Ukraine COUNTRY SE Sweden Kingdom of Sweden Sweden COUNTRY SE Sweden Kingdom of Sweden COUNTRY BS Bahamas Commonwealth of the Bahamas The Bahamas COUNTRY BS Bahamas Commonwealth of the Bahamas COUNTRY JP Japan Japan Japan COUNTRY JP Japan Japan COUNTRY KP North Korea Democratic People’s Republic of Korea North Korea COUNTRY KP North Korea Democratic People’s Republic of Korea COUNTRY CL Chile Republic of Chile Chile COUNTRY CL Chile Republic of Chile COUNTRY BR Brazil Federative Republic of Brazil Brazil COUNTRY BR Brazil Federative Republic of Brazil India COUNTRY CN China People’s Republic of China China COUNTRY CN China People’s Republic of China COUNTRY MX Mexico United Mexican States Mexico COUNTRY MX Mexico United Mexican States COUNTRY PA Panama Republic of Panama Panama COUNTRY PA Panama Republic of Panama COUNTRY HN Honduras Republic of Honduras Honduras COUNTRY HN Honduras Republic of Honduras COUNTRY CR Costa Rica Republic of Costa Rica Costa Rica COUNTRY CR Costa Rica Republic of Costa Rica COUNTRY EC Ecuador Republic of Ecuador Ecuador COUNTRY EC Ecuador Republic of Ecuador COUNTRY AR Argentina Argentine Republic Argentina COUNTRY AR Argentina Argentine Republic COUNTRY CO Colombia Republic of Colombia Colombia COUNTRY CO Colombia Republic of Colombia COUNTRY UY Uruguay Eastern Republic of Uruguay Uruguay COUNTRY UY Uruguay Eastern Republic of Uruguay COUNTRY VE Venezuela Bolivarian Republic of Venezuela Venezuela COUNTRY VE Venezuela Bolivarian Republic of Venezuela COUNTRY PE Peru Republic of Peru Peru COUNTRY PE Peru Republic of Peru COUNTRY PY Paraguay Republic of Paraguay Paraguay COUNTRY PY Paraguay Republic of Paraguay COUNTRY BZ Belize Belize Belize COUNTRY BZ Belize Belize COUNTRY SV El Salvador Republic of El Salvador El Salvador COUNTRY SV El Salvador Republic of El Salvador COUNTRY GT Guatemala Republic of Guatemala Guatemala COUNTRY GT Guatemala Republic of Guatemala COUNTRY FI Finland Republic of Finland Finland COUNTRY FI Finland Republic of Finland COUNTRY BE Belgium Kingdom of Belgium Belgium COUNTRY BE Belgium Kingdom of Belgium COUNTRY PL Poland Republic of Poland Poland COUNTRY PL Poland Republic of Poland COUNTRY FR France French Republic France COUNTRY FR France French Republic COUNTRY CH Switzerland Swiss Confederation Switzerland COUNTRY CH Switzerland Swiss Confederation COUNTRY AT Austria Republic of Austria Austria COUNTRY AT Austria Republic of Austria COUNTRY IE Ireland Ireland Ireland COUNTRY IE Ireland Ireland COUNTRY PT Portugal Portuguese Republic Portugal COUNTRY PT Portugal Portuguese Republic COUNTRY GR Greece Hellenic Republic Greece COUNTRY GR Greece Hellenic Republic COUNTRY LU Luxembourg Grand Duchy of Luxembourg Luxembourg COUNTRY LU Luxembourg Grand Duchy of Luxembourg COUNTRY AD Andorra Principality of Andorra Andorra COUNTRY AD Andorra Principality of Andorra COUNTRY BG Bulgaria Republic of Bulgaria Bulgaria COUNTRY BG Bulgaria Republic of Bulgaria COUNTRY RO Romania Romania Romania COUNTRY RO Romania Romania COUNTRY HU Hungary Hungary Hungary COUNTRY HU Hungary Hungary COUNTRY AL Albania Republic of Albania Albania COUNTRY AL Albania Republic of Albania COUNTRY CZ Czech Republic Czech Republic Czech Republic COUNTRY CZ Czech Republic Czech Republic COUNTRY SI Slovenia Republic of Slovenia Slovenia COUNTRY SI Slovenia Republic of Slovenia COUNTRY SK Slovakia Slovak Republic Slovakia COUNTRY SK Slovakia Slovak Republic COUNTRY RS Serbia Republic of Serbia Serbia COUNTRY RS Serbia Republic of Serbia COUNTRY LV Latvia Republic of Latvia ISO3166-2 codes for 2009 revision of admin. units seem not to have been assigned. Latvia COUNTRY LV Latvia Republic of Latvia COUNTRY EE Estonia Republic of Estonia Estonia COUNTRY EE Estonia Republic of Estonia COUNTRY LT Lithuania Republic of Lithuania Lithuania COUNTRY LT Lithuania Republic of Lithuania COUNTRY NI Nicaragua Republic of Nicaragua Nicaragua COUNTRY NI Nicaragua Republic of Nicaragua COUNTRY SM San Marino Republic of San Marino San Marino COUNTRY SM San Marino Republic of San Marino COUNTRY VA the Holy See/ Vatican City State the Holy See/ Vatican City State Vatican City COUNTRY VA the Holy See/ Vatican City State the Holy See/ Vatican City State COUNTRY ID Indonesia Republic of Indonesia Indonesia COUNTRY ID Indonesia Republic of Indonesia COUNTRY TH Thailand Kingdom of Thailand Thailand COUNTRY TH Thailand Kingdom of Thailand COUNTRY BD Bangladesh People’s Republic of Bangladesh Bangladesh COUNTRY BD Bangladesh People’s Republic of Bangladesh COUNTRY VN Vietnam Socialist Republic of Vietnam Viet Nam COUNTRY VN Vietnam Socialist Republic of Vietnam COUNTRY CU Cuba Republic of Cuba Cuba COUNTRY CU Cuba Republic of Cuba COUNTRY TT Trinidad and Tobago Republic of Trinidad and Tobago Trinidad and Tobago COUNTRY TT Trinidad and Tobago Republic of Trinidad and Tobago COUNTRY JM Jamaica Jamaica Jamaica COUNTRY JM Jamaica Jamaica COUNTRY MC Monaco Principality of Monaco Monaco COUNTRY MC Monaco Principality of Monaco COUNTRY LI Liechtenstein Principality of Liechtenstein Liechtenstein COUNTRY LI Liechtenstein Principality of Liechtenstein COUNTRY MD Moldova Republic of Moldova Moldova COUNTRY MD Moldova Republic of Moldova COUNTRY BN Brunei Brunei Darussalam Brunei Darussalam COUNTRY BN Brunei Brunei Darussalam COUNTRY MY Malaysia Malaysia Malaysia COUNTRY MY Malaysia Malaysia COUNTRY BT Bhutan Kingdom of Bhutan Bhutan COUNTRY BT Bhutan Kingdom of Bhutan COUNTRY PG Papua New Guinea Independent State of Papua New Guinea Papua New Guinea COUNTRY PG Papua New Guinea Independent State of Papua New Guinea COUNTRY SG Singapore Republic of Singapore Singapore COUNTRY SG Singapore Republic of Singapore COUNTRY LK Sri Lanka Democratic Socialist Republic of Sri Lanka Sri Lanka COUNTRY LK Sri Lanka Democratic Socialist Republic of Sri Lanka COUNTRY TL Timor-Leste Democratic Republic of Timor-Leste Timor COUNTRY TL Timor-Leste Democratic Republic of Timor-Leste COUNTRY EG Egypt Arab Republic of Egypt The 2nd level administrative regions of Egypt are very confusuing and different sources conflicting. Those in gaz.obo are from GeoHive (http://www.xist.org/default1.aspx) and are not fully in agreement with those from the WHO (the file EGY_SALB_table.xls downloaded from http://www.who.int/whosis/database/gis/salb/salb_coding.aspx#DATA). Egypt COUNTRY EG Egypt Arab Republic of Egypt COUNTRY DO Dominican Republic Dominican Republic Dominican Republic COUNTRY DO Dominican Republic Dominican Republic COUNTRY HT Haiti Republic of Haiti Haiti COUNTRY HT Haiti Republic of Haiti COUNTRY AM Armenia Republic of Armenia Armenia COUNTRY AM Armenia Republic of Armenia COUNTRY NP Nepal Federal Democratic Republic of Nepal Nepal COUNTRY NP Nepal Federal Democratic Republic of Nepal COUNTRY IR Iran Islamic Republic of Iran Iran COUNTRY IR Iran Islamic Republic of Iran COUNTRY IQ Iraq Republic of Iraq Iraq COUNTRY IQ Iraq Republic of Iraq COUNTRY PH Philippines Republic of the Philippines The Philippines COUNTRY PH Philippines Republic of the Philippines COUNTRY AZ Azerbaijan Republic of Azerbaijan Azerbaijan COUNTRY AZ Azerbaijan Republic of Azerbaijan COUNTRY GE Georgia Georgia begin_date: 1936-12-05. end_date: 1990-10-20. Georgia COUNTRY GE Georgia Georgia COUNTRY UZ Uzbekistan Republic of Uzbekistan begin_date: 1991-12-31. Uzbekistan COUNTRY UZ Uzbekistan Republic of Uzbekistan COUNTRY KZ Kazakhstan Republic of Kazakhstan Geographically the western regions of Kazakhstan may be in Europe. Kazakhstan COUNTRY KZ Kazakhstan Republic of Kazakhstan COUNTRY TM Turkmenistan Turkmenistan Turkmenistan COUNTRY TM Turkmenistan Turkmenistan COUNTRY PK Pakistan Islamic Republic of Pakistan Pakistan COUNTRY PK Pakistan Islamic Republic of Pakistan COUNTRY SA Saudi Arabia Kingdom of Saudi Arabia Saudi Arabia COUNTRY SA Saudi Arabia Kingdom of Saudi Arabia COUNTRY BH Bahrain Kingdom of Bahrain Bahrain COUNTRY BH Bahrain Kingdom of Bahrain COUNTRY AE United Arab Emirates United Arab Emirates United Arab Emirates COUNTRY AE United Arab Emirates United Arab Emirates COUNTRY OM Oman Sultanate of Oman Oman COUNTRY OM Oman Sultanate of Oman COUNTRY YE Yemen Republic of Yemen Yemen COUNTRY YE Yemen Republic of Yemen COUNTRY KW Kuwait State of Kuwait Kuwait COUNTRY KW Kuwait State of Kuwait COUNTRY QA Qatar State of Qatar Qatar COUNTRY QA Qatar State of Qatar COUNTRY TW Taiwan Taiwan Republic of China COUNTRY TW Taiwan Taiwan COUNTRY KM Comoros Union of the Comoros Comoros COUNTRY KM Comoros Union of the Comoros COUNTRY AF Afghanistan Islamic Republic of Afghanistan Afghanistan COUNTRY AF Afghanistan Islamic Republic of Afghanistan COUNTRY AG Antigua and Barbuda Antigua and Barbuda Antigua and Barbuda COUNTRY AG Antigua and Barbuda Antigua and Barbuda COUNTRY BY Belarus Republic of Belarus begin_date: 1990-07-27. Belarus COUNTRY BY Belarus Republic of Belarus COUNTRY BA Bosnia and Herzegovina Bosnia and Herzegovina Bosnia and Herzegovina COUNTRY BA Bosnia and Herzegovina Bosnia and Herzegovina COUNTRY KH Cambodia Kingdom of Cambodia Cambodia COUNTRY KH Cambodia Kingdom of Cambodia COUNTRY LA Laos Lao People’s Democratic Republic Laos COUNTRY LA Laos Lao People’s Democratic Republic COUNTRY DM Dominica Commonwealth of Dominica Dominica COUNTRY DM Dominica Commonwealth of Dominica COUNTRY FJ Fiji Republic of Fiji Fiji COUNTRY FJ Fiji Republic of Fiji Kyrgyzstan COUNTRY KG Kyrgyzstan Kyrgyz Republic Kiribati COUNTRY KG Kyrgyzstan Kyrgyz Republic COUNTRY MK Former Yugoslav Republic of Macedonia, the Former Yugoslav Republic of Macedonia, the. This code is in accordance with ISO 3166-2, code taken from name in Macedonian: Makedonija. Macedonia COUNTRY MK Former Yugoslav Republic of Macedonia, the Former Yugoslav Republic of Macedonia, the. This code is in accordance with ISO 3166-2, code taken from name in Macedonian: Makedonija. COUNTRY ME Montenegro Montenegro Montenegro COUNTRY ME Montenegro Montenegro COUNTRY MM Myanmar/Burma Myanmar/Burma Myanmar COUNTRY MM Myanmar/Burma Myanmar/Burma COUNTRY NR Nauru Republic of Nauru Nauru COUNTRY NR Nauru Republic of Nauru COUNTRY NU Niue Niue Niue Fekai COUNTRY NU Niue Niue COUNTRY PW Palau Republic of Palau Palau COUNTRY PW Palau Republic of Palau COUNTRY KN Saint Kitts and Nevis Federation of Saint Kitts and Nevis Saint Kitts-Nevis COUNTRY KN Saint Kitts and Nevis Federation of Saint Kitts and Nevis COUNTRY LC Saint Lucia Saint Lucia Saint Lucia COUNTRY LC Saint Lucia Saint Lucia COUNTRY AS American Samoa American Samoa: territory of the USA. Samoa COUNTRY AS American Samoa American Samoa: territory of the USA. COUNTRY TJ Tajikistan Republic of Tajikistan Tajikistan COUNTRY TJ Tajikistan Republic of Tajikistan COUNTRY TO Tonga Kingdom of Tonga Tonga COUNTRY TO Tonga Kingdom of Tonga COUNTRY VU Vanuatu Republic of Vanuatu Vanuatu COUNTRY VU Vanuatu Republic of Vanuatu COUNTRY ST São Tomé and Príncipe Democratic Republic of São Tomé and Príncipe Sao Tome and Principe COUNTRY ST São Tomé and Príncipe Democratic Republic of São Tomé and Príncipe COUNTRY MN Mongolia Mongolia Mongolia COUNTRY MN Mongolia Mongolia COUNTRY TV Tuvalu Tuvalu Tuvalu COUNTRY TV Tuvalu Tuvalu Kosovo begin_date: 1943-11-29. end_date: 1991-06-25. Previous to 1943: Kingdom of Yugoslavia, begins_in: 1918-12-01; end_date: 1941-04_17. [Former] Yugoslavia COUNTRY SS South Sudan Republic of South Sudan South Sudan COUNTRY SS South Sudan Republic of South Sudan COUNTRY TK Tokelau Tokelau: territory of New Zealand. Tokelau COUNTRY TK Tokelau Tokelau: territory of New Zealand. COUNTRY VC Saint Vincent and the Grenadines Saint Vincent and the Grenadines Saint Vincent and the Grenadines COUNTRY VC Saint Vincent and the Grenadines Saint Vincent and the Grenadines COUNTRY GD Grenada Grenada Grenada COUNTRY GD Grenada Grenada MTX A0C78 Gallus gallus broiler Gallus gallus animals raised for meat production purposes. The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Broiler broiler chickens MTX A0C9L Dairy cows Cattle having reached the physical maturity, for milk production. The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Dairy_cattle dairy cattle MTX A0C9Q Meat production cattle Cattle having reached the physical maturity, for meat production. The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Beef_cattle beef cattle Classification not possible ANLYMD_PRVAM F001A Classification not possible Analytical method measuring principle is known, but could not be classified. High Performance Liquid Chromatography (HPLC)/Liquid Chromatography (LC) ANLYMD_PRVAM F018A High Performance Liquid Chromatography (HPLC)/Liquid Chromatography (LC) High Performance, High Pressure and Liquid Chromatography. Immunological detection or quantification method ANLYMD_PRVAM F077A Immunological detection or quantification method Applies to e.g. immunoelectrophoresis Enzyme-linked immunosorbent assay (ELISA) ANLYMD_PRVAM F080A Enzyme-linked immunosorbent assay (ELISA) Enzyme-linked Immunosorbent Assay PCR ANLYMD_PRVAM F086A PCR Polymerase Chain Reaction Microscopical and histometrical tests ANLYMD_PRVAM F095A Microscopical and histometrical tests Microbiological tests ANLYMD_PRVAM F099A Microbiological tests Microbiological standard tests ANLYMD_PRVAM F100A Microbiological standard tests Applies to e.g. MPN Microbiological special tests ANLYMD_PRVAM F101A Microbiological special tests Applies to e.g. Keimdiff, Salm test, etc. Molecular detection or quantification method ANLYMD_PRVAM F115A Molecular detection or quantification method Morphological identification ANLYMD_PRVAM F120A Morphological identification Morphological identification for insect samples Indirect Immunofluorescent Antibody test (IFAT) ANLYMD_PRVAM F121A Indirect Immunofluorescent Antibody test (IFAT) A form of fluorescent antibody technique using antigen-antibody complex labelled with flourescein-conjugated anti-immunoglobulin antibody Real-time PCR (CEN TC275/WG6) ANLYMD_PRVAM F123A Real-time PCR (CEN TC275/WG6) Real-time polymerase chain reaction (quantitative PCR) AFNOR NF U47 100 (2007) ANLYMD_PRVAM F133A AFNOR NF U47 100 (2007) Isolation and identification of Salmonella or search for particular serovar's in the animal production sector AFNOR NF U47 101 (2007) ANLYMD_PRVAM F134A AFNOR NF U47 101 (2007) Isolation and identification of any Salmonella serotypes or of specified salmonella serotypes among birds ISO 16654:2001 ANLYMD_PRVAM F135A ISO 16654:2001 Horizontal method for the detection of Escherichia coli O157 ISO 20776-1:2006 ANLYMD_PRVAM F136A ISO 20776-1:2006 Reference method for testing the in vitro activity of antimicrobial agents against rapidly growing aerobic bacteria involved in infectious diseases ISO 6579:2002 ANLYMD_PRVAM F137A ISO 6579:2002 Horizontal method for the detection of Salmonella spp. ISO 6579:2002/Amd 1:2007 ANLYMD_PRVAM F138A ISO 6579:2002/Amd 1:2007 Annex D: Detection of Salmonella spp. in animal faeces and in environmental samples from the primary production stage NMKL 164, 2005, 2nd Ed. Escherichia coli O157 ANLYMD_PRVAM F139A NMKL 164, 2005, 2nd Ed. Escherichia coli O157 Detection of Escherichia coli serogroup O157 in foods and feeding stuffs NMKL 71, 1999, 5th Ed. Salmonella ANLYMD_PRVAM F140A NMKL 71, 1999, 5th Ed. Salmonella Detection of Salmonella in food Enumeration method ANLYMD_PRVAM F141A Enumeration method ISO 11290-2:1998 (Horizontal method for the detection and enumeration of Listeria monocytogenes -- Part 2: Enumeration method) and ISO 11290-2:1998/Amd 1:2004 (Modification of the enumeration medium ) Detection method of microorganisms ANLYMD_PRVAM F144A Detection method of microorganisms ISO 11290-1:1996 (Horizontal method for the detection and enumeration of Listeria monocytogenes -- Part 1: Detection method) and ISO 11290-1:1996/Amd 1:2004 (Modification of the isolation media and the haemolysis test, and inclusion of precision data ) Detection method presence in x g ANLYMD_PRVAM F145A Detection method presence in x g ISO 11290-1:1996 (Horizontal method for the detection and enumeration of Listeria monocytogenes -- Part 1: Detection method) and ISO 11290-1:1996/Amd 1:2004 (Modification of the isolation media and the haemolysis test, and inclusion of precision data ) Complement fixation test (CFT) ANLYMD_PRVAM F148A Complement fixation test (CFT) A serological test for detecting the presence of a specific antibody or antigen Modified agglutination test (MAT) ANLYMD_PRVAM F149A Modified agglutination test (MAT) Latex agglutination test (LAT) ANLYMD_PRVAM F150A Latex agglutination test (LAT) Immunoblotting (IB) ANLYMD_PRVAM F151A Immunoblotting (IB) Analytical technique used to detect specific proteins in the given sample of tissue homogenate or extract. Indirect ELISA (I-ELISA) ANLYMD_PRVAM F152A Indirect ELISA (I-ELISA) Fluorescent in situ hybridization (FISH) ANLYMD_PRVAM F153A Fluorescent in situ hybridization (FISH) A cytogenetic technique that is used to detect and localize the presence or absence of specific DNA sequences on chromosomes. Isolation (Cell, Egg, Mouse) ANLYMD_PRVAM F154A Isolation (Cell, Egg, Mouse) Immuno Histo Chemistry (IHC) ANLYMD_PRVAM F155A Immuno Histo Chemistry (IHC) Immunofluorenscence assay tests (IFA) ANLYMD_PRVAM F156A Immunofluorenscence assay tests (IFA) Staining ANLYMD_PRVAM F157A Staining Real-Time PCR (qualitative or quantitative) ANLYMD_PRVAM F159A Real-Time PCR (qualitative or quantitative) Direct agglutination (DA) ANLYMD_PRVAM F160A Direct agglutination (DA) EU RL method_food_2. Rev. 2 - O104:H4 ANLYMD_PRVAM F161A EU RL method_food_2. Rev. 2 - O104:H4 Detection and identification of Verocytotoxin-producing Escherichia coli (VTEC) O104:H4 in food by Real Time PCR Histology ANLYMD_PRVAM F162A Histology ISO 10272-1:2006 Campylobacter ANLYMD_PRVAM F163A ISO 10272-1:2006 Campylobacter Microbiology of food and animal feeding stuffs -- Horizontal method for detection and enumeration of Campylobacter spp. -- Part 1: Detection method ISO/TS 10272-2:2006 Campylobacter ANLYMD_PRVAM F164A ISO/TS 10272-2:2006 Campylobacter Microbiology of food and animal feeding stuffs -- Horizontal method for detection and enumeration of Campylobacter spp. -- Part 2: Colony-count technique ISO/TS 10272-3:2010 Campylobacter ANLYMD_PRVAM F165A ISO/TS 10272-3:2010 Campylobacter Microbiology of food and animal feeding stuffs -- Horizontal method for detection and enumeration of Campylobacter spp. -- Part 3: Semi-quantitative method ISO/TS 10272-3:2010/Cor 1:2011 Campylobacter ANLYMD_PRVAM F166A ISO/TS 10272-3:2010/Cor 1:2011 Campylobacter ISO 6579:2002 Salmonella ANLYMD_PRVAM F167A ISO 6579:2002 Salmonella Microbiology of food and animal feeding stuffs -- Horizontal method for the detection of Salmonella spp. ISO 6579:2002/Amd 1:2007 (Annex D of ISO 6579) Salmonella ANLYMD_PRVAM F168A ISO 6579:2002/Amd 1:2007 (Annex D of ISO 6579) Salmonella Annex D: Detection of Salmonella spp. in animal faeces and in environmental samples from the primary production stage ISO 11290-1:1996/Amd 1:2004 Listeria ANLYMD_PRVAM F169A ISO 11290-1:1996/Amd 1:2004 Listeria Modification of the isolation media and the haemolysis test, and inclusion of precision data ISO 11290-2:1998/Amd 1:2004 Listeria ANLYMD_PRVAM F170A ISO 11290-2:1998/Amd 1:2004 Listeria Modification of the enumeration medium EN ISO 6888-1:1999/Amdt 1:2003 Coagulase-positives staphylococci ANLYMD_PRVAM F171A EN ISO 6888-1:1999/Amdt 1:2003 Coagulase-positives staphylococci Inclusion of precision data EN ISO 6888-2:1999/Amdt 1:2003 Coagulase-positives staphylococci ANLYMD_PRVAM F172A EN ISO 6888-2:1999/Amdt 1:2003 Coagulase-positives staphylococci Inclusion of precision data ISO/TS 13136:2012 (including the EU-RL adaptation for O104:H4) ANLYMD_PRVAM F173A ISO/TS 13136:2012 (including the EU-RL adaptation for O104:H4) Microbiology of food and animal feed -- Real-time polymerase chain reaction (PCR)-based method for the detection of food-borne pathogens -- Horizontal method for the detection of Shiga toxin-producing Escherichia coli (STEC) and the determination of O157, ISO 16654:2001 E. coli ANLYMD_PRVAM F174A ISO 16654:2001 E. coli Microbiology of food and animal feeding stuffs -- Horizontal method for the detection of Escherichia coli O157 ISO 10273:2003 Yersinia ANLYMD_PRVAM F175A ISO 10273:2003 Yersinia Microbiology of food and animal feeding stuffs -- Horizontal method for the detection of presumptive pathogenic Yersinia enterocolitica EN/ISO 7932 Bacillus cereus ANLYMD_PRVAM F176A EN/ISO 7932 Bacillus cereus Microbiology of food and animal feeding stuffs -- Horizontal method for the enumeration of presumptive Bacillus cereus -- Colony-count technique at 30 degrees C ISO/TS 22964:2006 (IDF/RM 210: 2006) Cronobacter spp. (Enterobacter sakazakii) ANLYMD_PRVAM F177A ISO/TS 22964:2006 (IDF/RM 210: 2006) Cronobacter spp. (Enterobacter sakazakii) Milk and milk products -- Detection of Enterobacter sakazakii Sedimentation and Counting Technique ANLYMD_PRVAM F188A Sedimentation and Counting Technique Eckert J, Deplazes P, Craig PS, Gemmell MA, Gottstein B, Heath D, et al. Echinococcosis in animals: clinical aspects, diagnosis and treatment. In: Eckert J, Gemmell MA, F.-X. Meslin, Pawlowski ZS, editors. WHO/OIE Manual on echinococcosis in humans and an Reverse-transcription PCR (RT-PCR) ANLYMD_PRVAM F189A Reverse-transcription PCR (RT-PCR) IgG ELISA ANLYMD_PRVAM F190A IgG ELISA IgM-capture ELISA (MAC-ELISA) ANLYMD_PRVAM F191A IgM-capture ELISA (MAC-ELISA) Indirect hemoagglutination test (IHA) ANLYMD_PRVAM F192A Indirect hemoagglutination test (IHA) Seroneutralisation test ANLYMD_PRVAM F193A Seroneutralisation test Simplex PCR ANLYMD_PRVAM F194A Simplex PCR Duplex PCR ANLYMD_PRVAM F195A Duplex PCR Multiplex PCR ANLYMD_PRVAM F196A Multiplex PCR Multiple-locus variable-number tandem repeat analysis (MLVA) ANLYMD_PRVAM F197A Multiple-locus variable-number tandem repeat analysis (MLVA) Spa-typing ANLYMD_PRVAM F198A Spa-typing Multi locus sequence typing (MLST) ANLYMD_PRVAM F199A Multi locus sequence typing (MLST) Unknown ANLYMD_PRVAM F500A Unknown Analytical method unknown Pulsed field gel electrophoresis (PFGE) ANLYMD_PRVAM F504A Pulsed field gel electrophoresis (PFGE) Whole genome sequencing ANLYMD_PRVAM F512A Whole genome sequencing Rose Bengal plate test (RBT)/Buffered Brucella antigen test (BBAT) ANLYMD_PRVAM F520A Rose Bengal plate test (RBT)/Buffered Brucella antigen test (BBAT) Serum agglutination test (SAT) ANLYMD_PRVAM F521A Serum agglutination test (SAT) Milk ring-test ANLYMD_PRVAM F523A Milk ring-test ELISA, Competitive ELISA (C-ELISA) ANLYMD_PRVAM F530A ELISA, Competitive ELISA (C-ELISA) Macroscopic identification method ANLYMD_PRVAM F533A Macroscopic identification method Immunofluorescence method ANLYMD_PRVAM F537A Immunofluorescence method Fluorescence polarisation assay (FPA) ANLYMD_PRVAM F538A Fluorescence polarisation assay (FPA) Automatic digestion method for pooled samples of up to 35 g ANLYMD_PRVAM F543A Automatic digestion method for pooled samples of up to 35 g Magnetic stirrer method for pooled sample digestion ANLYMD_PRVAM F544A Magnetic stirrer method for pooled sample digestion Mechanically assisted pooled sample digestion method / on filter isolation technique ANLYMD_PRVAM F545A Mechanically assisted pooled sample digestion method / on filter isolation technique Trichinoscopic examination ANLYMD_PRVAM F546A Trichinoscopic examination Mechanically assisted pooled sample digestion method/sedimentation technique ANLYMD_PRVAM F547A Mechanically assisted pooled sample digestion method/sedimentation technique Combination disk method ANLYMD_PRVAM F555A Combination disk method Combination strip test/Epsilometer test ANLYMD_PRVAM F556A Combination strip test/Epsilometer test Skin test ANLYMD_PRVAM F567A Skin test Magnetic stirrer method for pooled sample digestion/on filter isolation and larva detection by a latex agglutination test ANLYMD_PRVAM F591A Magnetic stirrer method for pooled sample digestion/on filter isolation and larva detection by a latex agglutination test Artificial digestion test for in vivo detection of Trichinella spp. larvae in meat samples, PrioCheck Trichinella AAD Kit ANLYMD_PRVAM F592A Artificial digestion test for in vivo detection of Trichinella spp. larvae in meat samples, PrioCheck Trichinella AAD Kit ISO 16654:2001 or NMKL 164:2005 or DIN 10167 ANLYMD_PRVAM F593A ISO 16654:2001 or NMKL 164:2005 or DIN 10167 ISO 16654:2001 or NMKL 164:2005 or DIN 10167 or any alternative method validated against these methods, according to the ISO 16140. In case of testing E. coli O157 in animal faecal samples, also related OIE method is considered an alternative validated me In house real time PCR methods based on ISO/TS 13136:2012 ANLYMD_PRVAM F594A In house real time PCR methods based on ISO/TS 13136:2012 In house real time PCR methods based on ISO/TS 13136:2012 or any alternative method validated against this method, according to the ISO 16140 or PCR methods based on ISO/TS 13136:2012, adapted to animal samples. Other methods based on PCR detection of vtx genes ANLYMD_PRVAM F595A Other methods based on PCR detection of vtx genes DIN 10118:2004 ANLYMD_PRVAM F596A DIN 10118:2004 DIN 10118:2004 or any alternative method validated against this method, according to the ISO 16140 Other methods based on the immunochemical detection of VT ANLYMD_PRVAM F597A Other methods based on the immunochemical detection of VT Unspecified ANLYMD_PRVAM F598A Unspecified NMKL 119, 2007, 3rd Ed. Termotolerante Campylobacter ANLYMD_PRVAM F600A NMKL 119, 2007, 3rd Ed. Termotolerante Campylobacter NMKL No. 119, 3rd ed. 2007, Thermotolerant Campylobacter. Detection, semi-quantitative and quantitative determination in foods and drinking water NMKL 187, 2007 Salmonella ANLYMD_PRVAM F601A NMKL 187, 2007 Salmonella NMKL No. 187, 2007, Salmonella. Detection in foods, animal faeces and environmental materials from primary animal production using MSRV OIE method for E.coli O157 in animal faecal samples ANLYMD_PRVAM F602A OIE method for E.coli O157 in animal faecal samples OIE recommended method for the detection of E.coli O157 in animal faeces and any other cultural methods based on ISO 16654/2001 adapted to animal samples ISO 6579-1:2017 Salmonella ANLYMD_PRVAM F609A ISO 6579-1:2017 Salmonella Microbiology of the food chain -- Horizontal method for the detection, enumeration and serotyping of Salmonella -- Part 1: Detection of Salmonella spp. ISO 11290-1:2017 Listeria ANLYMD_PRVAM F610A ISO 11290-1:2017 Listeria Microbiology of the food chain -- Horizontal method for the detection and enumeration of Listeria monocytogenes and of Listeria spp. -- Part 1: Detection method ISO 11290-2:2017 Listeria ANLYMD_PRVAM F611A ISO 11290-2:2017 Listeria Microbiology of the food chain -- Horizontal method for the detection and enumeration of Listeria monocytogenes and of Listeria spp. -- Part 2: Enumeration method ISO 19020:2017 Staphylococcal enterotoxins ANLYMD_PRVAM F612A ISO 19020:2017 Staphylococcal enterotoxins Microbiology of the food chain -- Horizontal method for the immunoenzymatic detection of staphylococcal enterotoxins in foodstuffs ISO 21528-1:2017 Enterobacteriaceae ANLYMD_PRVAM F613A ISO 21528-1:2017 Enterobacteriaceae Microbiology of the food chain -- Horizontal method for the detection and enumeration of Enterobacteriaceae -- Part 1: Detection of Enterobacteriaceae ISO 21528-2:2017 Enterobacteriaceae ANLYMD_PRVAM F614A ISO 21528-2:2017 Enterobacteriaceae Microbiology of the food chain -- Horizontal method for the detection and enumeration of Enterobacteriaceae -- Part 2: Colony-count technique ISO 22964:2017 Cronobacter ANLYMD_PRVAM F615A ISO 22964:2017 Cronobacter Microbiology of the food chain -- Horizontal method for the detection of Cronobacter spp. ISO 10272-2:2017 Campylobacter ANLYMD_PRVAM F616A ISO 10272-2:2017 Campylobacter Microbiology of the food chain -- Horizontal method for detection and enumeration of Campylobacter spp. -- Part 2: Colony-count technique ISO 10272-1:2017 Campylobacter ANLYMD_PRVAM F617A ISO 10272-1:2017 Campylobacter Microbiology of the food chain -- Horizontal method for detection and enumeration of Campylobacter spp. -- Part 1: Detection method ISO 10273:2017 Yersinia enterocolitica ANLYMD_PRVAM F618A ISO 10273:2017 Yersinia enterocolitica Microbiology of the food chain -- Horizontal method for the detection of pathogenic Yersinia enterocolitica ISO 15216-1:2017 Hepatitis A virus and norovirus ANLYMD_PRVAM F619A ISO 15216-1:2017 Hepatitis A virus and norovirus Microbiology of the food chain -- Horizontal method for determination of hepatitis A virus and norovirus using real-time RT-PCR -- Part 1: Method for quantificatation ISO 19343:2017 Histamine ANLYMD_PRVAM F620A ISO 19343:2017 Histamine Microbiology of the food chain -- Detection and quantification of histamine in fish and fishery products -- HPLC method Visual inspection ANLYMD_PRVAM F648A Visual inspection Post-mortem inspection of carcases carryout according to the Regulation (EC) No 854/2004 NMKL 136, 5th ed. 2010, Listeria monocytogenes ANLYMD_PRVAM F649A NMKL 136, 5th ed. 2010, Listeria monocytogenes NMKL 136, 5th ed. 2010, Listeria monocytogenes. Detection in foods and feeding stuffs and enumeration in foods Slide agglutination according White Kauffmann Le Minor Scheme ANLYMD_PRVAM F650A Slide agglutination according White Kauffmann Le Minor Scheme Slide agglutination followed by molecular serotyping (PCR or WGS) ANLYMD_PRVAM F651A Slide agglutination followed by molecular serotyping (PCR or WGS) Flotation technique for faecal parasites ANLYMD_PRVAM F652A Flotation technique for faecal parasites Real-time PCR (BAX): detection of STEC and identification of serogroups O26, O111, O121, O145, O103 and O45 ANLYMD_PRVAM F653A Real-time PCR (BAX): detection of STEC and identification of serogroups O26, O111, O121, O145, O103 and O45 Detection ANLYTYP AT01A Detection Serotyping ANLYTYP AT02A Serotyping Phagetyping ANLYTYP AT03A Phagetyping Susceptibility test ANLYTYP AT04A Susceptibility test Speciation ANLYTYP AT05A Speciation Screening ANLYTYP AT06A Screening Quantification ANLYTYP AT07A Quantification Confirmation ANLYTYP AT08A Confirmation Determination ANLYTYP AT09A Determination Enumeration ANLYTYP AT10A Enumeration Isolate characterisation ANLYTYP AT11A Isolate characterisation Discriminatory test ANLYTYP AT12A Discriminatory test Molecular characterisation/genotyping ANLYTYP AT13A Molecular characterisation/genotyping Cyprus COUNTRY CY Cyprus Republic of Cyprus European Union non European Union broiler chickens MTX A0C78 Gallus gallus broiler Gallus gallus animals raised for meat production purposes. The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Broiler dairy cattle MTX A0C9L Dairy cows Cattle having reached the physical maturity, for milk production. The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Dairy_cattle beef cattle MTX A0C9Q Meat production cattle Cattle having reached the physical maturity, for meat production. The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Beef_cattle Bulgarian LANG BG Bulgarian Czech LANG CS Czech Danish LANG DA Danish German LANG DE German Greek LANG EL Greek English LANG EN English Spanish LANG ES Spanish Estonian LANG ET Estonian Finnish LANG FI Finnish French LANG FR French Irish LANG GA Irish Croatian LANG HR Croatian Hungarian LANG HU Hungarian Icelandic LANG IS Icelandic Italian LANG IT Italian Lithuanian LANG LT Lithuanian Latvian LANG LV Latvian Montenegrin LANG ME Montenegrin Macedonian LANG MK Macedonian Maltese LANG MT Maltese Dutch LANG NL Dutch Norwegian LANG NO Norwegian Polish LANG PL Polish Portuguese LANG PT Portuguese Romanian LANG RO Romanian Serbian LANG RS Serbian Russian LANG RU Russian Slovakian LANG SK Slovakian Slovene LANG SL Slovene Swedish LANG SV Swedish Turkish LANG TR Turkish Chinese LANG ZH Chinese animal sample MTXTYP S000A food sample MTXTYP S019A food stimulant MTXTYP S023A feed sample MTXTYP Environmental sample MTXTYP S027A unknown MTXTYP S030A Contact material MTXTYP S031A Human (as organism) MTX A056J Human (as organism) Humans as living organisms of the taxonomic group Homo sapiens (family Hominidae). The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Human Cattle (as animal) MTX A057E Cattle (as animal) Live animal of the taxonomic species Bos taurus Bojanus. The animals are commonly known as Cattle. The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Cattle Pig (as animal) MTX A057F Pig (as animal) Live animals of the taxonomic species Sus domestica L., Sus scrofa domesticus L. The animals are commonly known as Pig or swine. The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Domestic_pig Gallus gallus (chicken) (as animal) MTX A057Z Gallus gallus (chicken) (as animal) Live animal of the taxonomic species Gallus gallus domesticus L. The animals are commonly known as Gallus gallus (chicken) or Fowl or Chicken. The part considered is by default the whole living organism.£https://en.wikipedia.org/wiki/Chicken Campylobacter upsaliensis PARAM RF-00000043-MCG Campylobacter unspecified sp. PARAM RF-00000044-MCG Campylobacter rectus PARAM RF-00000045-MCG Campylobacter mucosalis PARAM RF-00000047-MCG Campylobacter lari PARAM RF-00000048-MCG Campylobacter curvus PARAM RF-00000049-MCG Campylobacter cryaerophilus PARAM RF-00000050-MCG Campylobacter hominis PARAM RF-00000051-MCG thermotolerant Campylobacter unspecified PARAM RF-00000052-MCG Campylobacter gracilis PARAM RF-00000053-MCG Campylobacter coli PARAM RF-00000054-MCG Campylobacter fetus PARAM RF-00000055-MCG Campylobacter fetus subsp. fetus PARAM RF-00000056-MCG Campylobacter fetus subsp. venerealis PARAM RF-00000057-MCG Campylobacter hyointestinalis PARAM RF-00000058-MCG Campylobacter hyointestinalis subsp. lawsonii PARAM RF-00000059-MCG Campylobacter hyointestinalis subsp. hyointestinalis PARAM RF-00000060-MCG Campylobacter jejuni PARAM RF-00000061-MCG Campylobacter jejuni subsp. jejuni PARAM RF-00000062-MCG Campylobacter sputorum PARAM RF-00000064-MCG Campylobacter sputorum subsp. bubulus PARAM RF-00000065-MCG Campylobacter sputorum subsp. mucosalis PARAM RF-00000066-MCG Campylobacter sputorum biovar sputorum PARAM RF-00000067-MCG Escherichia coli, non-pathogenic PARAM RF-00000125-MCG Escherichia coli, non-pathogenic Escherichia coli O26 Escherichia coli O26:H11 Escherichia coli O26:NM PARAM RF-00000139-MCG VTEC O26 Escherichia coli O145:NM PARAM RF-00000155-MCG VTEC O145 Escherichia coli O103 Escherichia coli O103:H11 Escherichia coli O103:H2 Escherichia coli O103:H25 PARAM RF-00000175-MCG VTEC O103 Escherichia coli O121:H19 PARAM RF-00000177-MCG VTEC O121 Escherichia coli O113:H21 PARAM RF-00000181-MCG VTEC O113 Escherichia coli O111 PARAM RF-00000182-MCG VTEC O111 Escherichia coli O128:H2 PARAM RF-00000184-MCG VTEC O128 VTEC non-O157 PARAM RF-00000193-MCG VTEC non-O157 Escherichia coli O157 PARAM RF-00000202-MCG VTEC O157 Salmonella spp PARAM RF-00000304-MCG Salmonella enterica subsp. enterica serovar Javiana PARAM RF-00000895-MCG Salmonella enterica subsp. enterica serovar Newport PARAM RF-00000960-MCG Salmonella enterica subsp. enterica serovar Virchow PARAM RF-00001152-MCG Salmonella enterica subsp. enterica serovar Stanley PARAM RF-00001316-MCG Salmonella bongori PARAM RF-00001328-PAR Salmonella enterica subsp. enterica serovar Hadar PARAM RF-00001843-MCG Salmonella enterica subsp. enterica serovar Infantis PARAM RF-00001894-MCG Salmonella enterica subsp. enterica serovar Heidelberg PARAM RF-00001957-MCG Salmonella enterica subsp. enterica serovar Enteritidis PARAM RF-00002135-MCG Salmonella enterica subsp. enterica serovar Typhimurium PARAM RF-00002265-MCG Escherichia coli O142:H6 PARAM RF-00002684-PAR VTEC O142 Salmonella enterica subsp. enterica PARAM RF-00003052-MCG Escherichia coli PARAM RF-00003072-PAR Salmonella enterica PARAM RF-00003200-PAR Escherichia coli O18 PARAM RF-00003235-PAR VTEC O18 Escherichia coli O45:H2 PARAM RF-00003254-PAR VTEC O45 Escherichia coli 151_06 PARAM RF-00003301-PAR VTEC O151 Escherichia coli, non-pathogenic, unspecified PARAM RF-00003897-MCG Escherichia coli, non-pathogenic, unspecified Official (National) programme PRGTYP K005A Official (National) programme Official (EU) programme PRGTYP K009A Official (EU) programme Diet study PRGTYP K010A Diet study Industry/ private programme PRGTYP K012A Industry/ private programme Survey PRGTYP K013A Survey Other/ Combination of several programmes PRGTYP K014A Other/ Combination of several programmes Official (National and EU) programme PRGTYP K018A Official (National and EU) programme EU increased control programme on imported food PRGTYP K019A EU increased control programme on imported food Clinical investigations PRGTYP K020A Clinical investigations Control and eradication programmes PRGTYP K021A Control and eradication programmes Monitoring PRGTYP K022A Monitoring Monitoring - active PRGTYP K023A Monitoring - active Monitoring - passive PRGTYP K024A Monitoring - passive Monitoring - EFSA specifications PRGTYP K025A Monitoring - EFSA specifications Surveillance PRGTYP K026A Surveillance Survey - EU baseline survey PRGTYP K027A Survey - EU baseline survey Survey - national survey PRGTYP K028A Survey - national survey Unspecified PRGTYP K029A Unspecified Surveillance active PRGTYP K030A Surveillance active Surveillance passive PRGTYP K031A Surveillance passive Outbreak investigation PRGTYP K032A Outbreak investigation RASSF alert notification PRGTYP K033A RASSF alert notification Industry sampling SAMPLR CX01A Industry sampling Sampling performed by the industry. Official sampling SAMPLR CX02A Official sampling Sampling performed under the control of the competent authority. Official and industry sampling SAMPLR CX03A Official and industry sampling Sampling performed under the control of the competent authority and by industry. HACCP and own check SAMPLR CX04A HACCP and own check Programme designed to effectively control processes by identifying critical control points (CCPs), establishing critical limits for each CCP, monitoring CCPs, gathering data, keeping records, and implementing corrective actions and verification procedures. HACCP is applied by the food or feed business operators (Codex Alimentarius). Private sampling SAMPLR CX05A Private sampling Sampling performed by private people/entities like pet owner, farmer, pet shop employee, private veterinarian (on request of a farmer or a pet owner or another private entity). Private sampler should be used in the following cases: the owner of a pet who takes a sample from its clinical suspected pet animal; the owner or vet of a zoo/circus who collects samples from animals of the zoo/circus to be diagnosed for a specific disease. Private sampler should not be used when veterinarians/owner/hunters are commissioned by the Competent Authorities or perform sampling within a specific legislation and for which a pre-determined sampling programme for monitoring/surveillance exists (in this case the sampler should be ‘Official sampling’). Official, based on Regulation 854/2004 SAMPLR CX06A Official, based on Regulation 854/2004 Official, based on Regulation 854/2004 Not applicable SAMPLR CX99A Not applicable Border inspection activities SAMPNT E010A Border inspection activities Veterinary activities SAMPNT E011A Veterinary activities Zoo SAMPNT E012A Zoo Veterinary clinics SAMPNT E013A Veterinary clinics Unspecified SAMPNT E098A Unspecified Others SAMPNT E099A Others Primary production SAMPNT E100A Primary production Farm SAMPNT E101A Farm Growing crops SAMPNT E110A Growing crops Bee hives SAMPNT E112A Bee hives Rearing of animals SAMPNT E120A Rearing of animals Breeding SAMPNT E121A Breeding Support activities to agriculture SAMPNT E130A Support activities to agriculture Support activities for crop production SAMPNT E131A Support activities for crop production Artificial insemination station SAMPNT E132A Artificial insemination station Other animal production support activity SAMPNT E139A Other animal production support activity Fishery activities SAMPNT E150A Fishery activities Fishing and fish processing SAMPNT E151A Fishing and fish processing Aquaculture SAMPNT E152A Aquaculture Fishing SAMPNT E153A Fishing Hatchery SAMPNT E160A Hatchery Game handling estabilishment SAMPNT E170A Game handling estabilishment Hunting SAMPNT E180A Hunting Wildlife research station SAMPNT E190A Wildlife research station Natural habitat SAMPNT E191A Natural habitat Hospital or medical care facility SAMPNT E210A Hospital or medical care facility Residential institution (nursing home or prison or boarding school) SAMPNT E220A Residential institution (nursing home or prison or boarding school) Household SAMPNT E230A Household School or kindergarten SAMPNT E240A School or kindergarten Manufacturing SAMPNT E300A Manufacturing Processing plant SAMPNT E301A Processing plant Meat processing SAMPNT E310A Meat processing Slaughterhouse SAMPNT E311A Slaughterhouse Cutting plant SAMPNT E312A Cutting plant Meat mincing SAMPNT E313A Meat mincing Meat preparing SAMPNT E314A Meat preparing Mechanical separation of meat SAMPNT E315A Mechanical separation of meat Other meat processing activities SAMPNT E319A Other meat processing activities Fish processing SAMPNT E320A Fish processing Fish freezing SAMPNT E321A Fish freezing Fish processing activities, other than freezing SAMPNT E329A Fish processing activities, other than freezing Manufacture of prepared animal feeds SAMPNT E350A Manufacture of prepared animal feeds Manufacture of compound feedingstuffs SAMPNT E351A Manufacture of compound feedingstuffs Manufacture of feed additives and pre-mixtures SAMPNT E352A Manufacture of feed additives and pre-mixtures Manufacture of prepared pet foods SAMPNT E353A Manufacture of prepared pet foods Feed mill SAMPNT E354A Feed mill Other processing activities SAMPNT E355A Other processing activities Water collection or treatment or supply SAMPNT E400A Water collection or treatment or supply Water distribution system SAMPNT E410A Water distribution system Water source SAMPNT E420A Water source Water treatment plant SAMPNT E430A Water treatment plant Distribution: wholesale and retail sale SAMPNT E500A Distribution: wholesale and retail sale Wholesale SAMPNT E510A Wholesale Retail SAMPNT E520A Retail Import activities SAMPNT E530A Import activities Packing centre SAMPNT E600A Packing centre Re-wrapping centre SAMPNT E610A Re-wrapping centre Storage SAMPNT E700A Storage Cold storage SAMPNT E710A Cold storage Conservation facilities SAMPNT E720A Conservation facilities Transport SAMPNT E800A Transport Road transport SAMPNT E810A Road transport Rail transport SAMPNT E820A Rail transport Water transport SAMPNT E830A Water transport Air transport SAMPNT E840A Air transport Travel abroad SAMPNT E850A Travel abroad Catering SAMPNT E900A Catering Restaurant or Cafe or Pub or Bar or Hotel or Catering service SAMPNT E910A Restaurant or Cafe or Pub or Bar or Hotel or Catering service Mobile retailer or market/street vendor SAMPNT E920A Mobile retailer or market/street vendor Take-away or fast-food outlet SAMPNT E930A Take-away or fast-food outlet Canteen or workplace catering SAMPNT E940A Canteen or workplace catering Temporary mass catering (fairs or festivals) SAMPNT E950A Temporary mass catering (fairs or festivals) Camp or picnic SAMPNT E960A Camp or picnic Disseminated cases SAMPNT E970A Disseminated cases Multiple places of exposure in one country SAMPNT E971A Multiple places of exposure in one country Multiple places of exposure in more than one country SAMPNT E972A Multiple places of exposure in more than one country Unknown SAMPNT E980A Unknown Nursery SAMPNT E981A Nursery Automatic distribution system for raw milk SAMPNT E982A Automatic distribution system for raw milk Official kennel SAMPNT E983A Official kennel Catering on aircraft or ship or train SAMPNT E990A Catering on aircraft or ship or train Objective sampling SAMPSTR ST10A Objective sampling Objective sampling—planned strategy based on the selection of a random sample, which is statistically representative of the population to be analysed. Each unit, within the framework population, has a specified probability of being selected. This strategy provides data from which statistical inference can be implemented. That means that the results inferred are comparable. Objective sampling is often the case in monitoring and surveillance schemes as well as in surveys. Selective sampling SAMPSTR ST20A Selective sampling Selective sampling—planned strategy whereby the selection of the sample is from previously defined ‘high-risk’ population groups. Samples are normally selected to either illustrate or document unsatisfactory conditions or suspected adulteration of a product. The sampling is deliberately biased and is directed at the particular products or manufacturers. The sampling procedure can be random or not. The specification of the ‘high-risk’ population comes from either scientific studies or previous analysis and information of other regions or countries. The comparability of the results lies on both the definition of the population to be analysed and the way the samples have been drawn Suspect sampling SAMPSTR ST30A Suspect sampling Suspect sampling—unplanned selection of a sample whereby the individual units are selected based on the recent judgement and experience regarding the population, lot or sampling frame, e.g. earlier positive samples. The samples obtained from this procedure are not randomly extracted. Convenient sampling SAMPSTR ST40A Convenient sampling Convenient sampling—is used in exploratory research when the researcher is interested in getting an inexpensive approximation of the truth. The samples are selected because they are convenient and easy to obtain. This non-probability method is often used during preliminary research efforts to get a gross estimate of the results, without incurring the cost or time required to select a random sample. This methodology is potentially subject to serious bias Census SAMPSTR ST50A Census Census—strategy whereby all units of the population are sampled Import sampling SAMPSTR ST60A Import sampling Other SAMPSTR ST90A Other Not specified SAMPSTR STXXA Not specified holding SAMPUNTYP G198A holding animal SAMPUNTYP G199A animal slaughter batch SAMPUNTYP G200A slaughter batch slaughter animal (heads) SAMPUNTYP G201A slaughter animal (heads) herd/flock SAMPUNTYP G202A herd/flock single SAMPUNTYP G203A single batch SAMPUNTYP G204A batch pen SAMPUNTYP G243A pen Cross-contamination is the contamination occurring during preparation for consumption of a food item by direct or indirect contact with another food item, equipment and work surfaces, including hands. For example, raw fruits and vegetables can contaminate cooked foods if they are not properly cleaned. In addition, juices from raw meat and poultry which come in contact with ready-to-eat foods can contaminate the cooked foods. Unwashed hands, unclean utensils and food contact surfaces result in a cross-contamination of food if that food is handled on these surfaces, with these utensils or processed by unwashed hands. Cross-contamination ZOO_CAT_CONFACT CF01A Cross-contamination Chilling is the process of cooling the food. Food is chilled inadequately if the core temperature of the food remains, for example, higher than 2–8°C for too long, which can result in multiplication of microorganisms. Please note that the sufficient chilling temperature is dependent on the type of food. For example, there are slight differences between minced meat and cheese. It is important that the core of the food will reach the appropriate cold temperature as quickly as possible. Inadequate chilling ZOO_CAT_CONFACT CF02A Inadequate chilling Inadequate heat treatment in terms of cooking can be defined as foods that are cooked at an inappropriate temperature for a suitable period of time or cooked at an appropriate temperature for an unsuitable period of time or cooked at an inappropriate temperature for an unsuitable period of time.Inadequate heat treatment can occur during the cooking or reheating of the incriminated food. This is the case if food is cooked at an inadequate temperature (for example < 70°C) and\/or for an inadequate period of time or the heat treatment of the core of the food is insufficient to kill the pathogenic microorganisms. Inadequate heat treatment ZOO_CAT_CONFACT CF03A Inadequate heat treatment An infected food handler is defined as cook or kitchen worker with a confirmed infection (regardless of symptomatic or asymptomatic infection) transmitting the causative agent onto food. In practice it is often impossible to differentiate whether the infection of the food handler occurred first and is the source of infection or if the food handler acquired the infection from the food. Please choose this category only if it is likely that the infected food handler is the source of infection. Infected food handler ZOO_CAT_CONFACT CF04A Infected food handler ‘Other’ can be chosen if the contributory factor identified during the outbreak investigation is not listed in the catalogue. Other contributory factor ZOO_CAT_CONFACT CF05A Other contributory factor When the time\/temperature abuse occurred during the storage of food. This applies to mistakes during hot holding of food or during the cold chain. If the food is held hot at an improper holding temperature (e.g. < 60°C) for an unsuitable period of time the likelihood of multiplication of microorganisms present on\/in the food is high. The cold chain, on the other hand, is the sequence of temperature-controlled operations after initial harvesting, and including chilled transport, cooling during and after production, chilled storage distribution and retailing, through to domestic storage until preparation for final consumption. If there is, for example, an interruption within the cold chain it can lead to a multiplication of microorganisms present on\/in the food. In addition, if food is stored in large containers or stacked too tightly the core of the food may not reach the appropriate cooling temperature. Storage time/temperature abuse ZOO_CAT_CONFACT CF06A Storage time/temperature abuse This option should chosen if no contributory factor has been identified during the investigation of the outbreak. Unknown ZOO_CAT_CONFACT CF07A Unknown Unprocessed contaminated ingredients are raw ingredients contaminated with the causative agents at the primary production level, during processing or transportation. The contamination occurs before preparation and consumption. Examples are eggs or meats that are contaminated with Salmonella. In addition, herbs that may have been contaminated with microbes during irrigation or by wild animals are often used in salads or added to ready-to-eat meals without further heating. Unprocessed contaminated ingredient ZOO_CAT_CONFACT CF08A Unprocessed contaminated ingredient A failure in the water treatment system is leading to contamination in the water supply. Drinking water treatment failures can have their origin in different areas like a failure of water treatment or disinfection, contamination of the water supply; or clusters of illness potentially caused by the former. Water treatment failure ZOO_CAT_CONFACT CF09A Water treatment failure Untreated drinking water is defined as non-potable water that has not been subjected to any process designed to remove contaminants or organisms. Untreated drinking water ZOO_CAT_CONFACT CF10A Untreated drinking water Analytical epidemiological evidence: a statistically significant association between consumption of a foodstuff and being a case in an analytical epidemiological study (e.g. cohort or case–control study). Analytical epidemiological evidence ZOO_CAT_EVDNC EV01A Analytical epidemiological evidence Descriptive epidemiological evidence: suspicion of a food vehicle in an outbreak based on the identification of common food exposures, from the systematic evaluation of cases and their characteristics and food histories over the likely incubation period by standardised means (such as standard questionnaires) from all, or an appropriate subset of, cases. Descriptive epidemiological evidence ZOO_CAT_EVDNC EV02A Descriptive epidemiological evidence Detection of causative agent in food chain or its environment - Detection of indistinguishable causative agent in humans Detection of causative agent in food chain or its environment - Detection of indistinguishable causative agent in humans ZOO_CAT_EVDNC EV03A Detection of causative agent in food chain or its environment - Detection of indistinguishable causative agent in humans Detection of causative agent in food chain or its environment - Symptoms and onset of illness pathognomonic to causative agent Detection of causative agent in food chain or its environment - Symptoms and onset of illness pathognomonic to causative agent ZOO_CAT_EVDNC EV04A Detection of causative agent in food chain or its environment - Symptoms and onset of illness pathognomonic to causative agent Detection of causative agent in food vehicle or its component - Symptoms and onset of illness pathognomonic to causative agent Detection of causative agent in food vehicle or its component - Symptoms and onset of illness pathognomonic to causative agent ZOO_CAT_EVDNC EV05A Detection of causative agent in food vehicle or its component - Symptoms and onset of illness pathognomonic to causative agent Detection of causative agent in food vehicle or its component - Detection of indistinguishable causative agent in humans Detection of causative agent in food vehicle or its component - Detection of indistinguishable causative agent in humans ZOO_CAT_EVDNC EV06A Detection of causative agent in food vehicle or its component - Detection of indistinguishable causative agent in humans Unknown Unknown ZOO_CAT_EVDNC EV07A Unknown Descriptive environmental evidence: e.g. evidence from food hygiene inspections. Descriptive environmental evidence ZOO_CAT_EVDNC EV08A Descriptive environmental evidence Product-tracing investigation: investigation to follow the movement of a food product and its constituents through the stages of production, processing and distribution, both backward and forward. Trace-back is the ability to trace a food product from the point of sale back to the source (ultimately the farm). Conversely, trace-forward is the ability to trace a food product from the source (ultimately the farm) forward to the point of sale. Product tracing may encompass trace-back and trace-forward. Product-tracing investigations ZOO_CAT_EVDNC EV09A Product-tracing investigations Fresh meat is meat that has not undergone any preserving process other than chilling, freezing or quick-freezing, including meat that is vacuum-wrapped or wrapped in a controlled atmosphere (Regulation (EC) No 853\/2004). Meat preparations are defined as fresh meat, including meat that has been reduced to fragments, which has had foodstuffs, seasonings or additives added to it or which has undergone processes insufficient to modify the internal muscle fibre structure of the meat and thus to eliminate the characteristics of fresh meat (Regulation (EC) No 853\/2004). Minced meat is boned meat that has been minced into fragments and contains less than 1 % salt (Regulation (EC) No 853\/2004), for example steak tartare. Meat products are defined as processed products resulting from the processing of meat or from further processing of such processed products, so that the cut surface shows that the product no longer has the characteristics of fresh meat (Regulation (EC) No 853\/2004). Meat and meat products ZOO_CAT_FOODVH A01QR Meat and meat products This category should be chosen if the implicated food is not identified. Unknown ZOO_CAT_FOODVH B00000B Unknown The following products shall be considered as drinking milk: raw milk intended for direct human consumption: milk, which has not been heated above 40°C or subjected to treatment having equivalent effect and intended to consumed raw; pasteurised milk: milk heat treated to destroy disease-causing bacteria; ultra-high temperature (UHT) milk: milk heated for a short time, around 1–2 seconds, at a temperature exceeding 135°C, which is the temperature required to kill spores in milk. Please specify the species of origin of the milk (such as cow, goat, sheep) as well as the treatment of the milk in the free text data element (for example: ‘raw goat milk’, ‘pasteurised cow milk’ or ‘UHT milk’). Please specify the species of origin of the milk (such as cow, goat, sheep) as well as the treatment of the milk in the free text data element (for example: ‘raw goat milk’, ‘pasteurised cow milk’ or ‘UHT milk’). Milk ZOO_CAT_FOODVH B07727B Milk Dairy products are defined as processed products resulting from the processing of raw milk or from the further processing of such processed products (Regulation (EC) No 853\/2004). Examples for dairy products are cream, buttermilk, milk powder, butter, yoghurt, ice cream and puddings made from milk. Dairy products (other than cheeses) ZOO_CAT_FOODVH B09607B Dairy products (other than cheeses) Cheese is the ripened or unripened soft, semi-soft, hard, or extra-hard product of milk, which may be coated, and in which the whey protein\/casein ratio does not exceed that of milk, obtained by coagulating of milk or protein of milk and\/or products obtained from milk which give an end product with similar characteristics. Please specify the species of origin of the milk (such as cow, goat, sheep) as well as whether the cheese was made from raw, low-heat-treated milk or pasteurised milk. In addition, the main type of cheese (hard, semi-soft or soft) and, if possible, also a detailed type (e.g. Camembert), if possible, in the free text data element. For example: ‘soft cheese made from raw goats’ milk’. Cheese ZOO_CAT_FOODVH B09627B Cheese Eggs are defined as eggs in shell that are produced by farmed birds and are fit for direct human consumption or for the preparation of egg products. Egg products are processed products resulting from the processing of eggs or of various components or mixtures of eggs or from the further processing of such processed products (Regulation (EC) No 853\/2004). Examples of egg products include:Liquid egg products: the purified whole egg, egg yolk or egg white is pasteurised and chemically preserved (e.g. by addition of salt). Frozen egg products: the purified whole egg, egg yolk or egg white is pasteurised and frozen. Dried and\/or heat-coagulated egg products: sugars are removed from the purified whole egg, egg yolk or egg white, which is then pasteurised and dried. Preserved eggs, including alkaline, salted and canned eggs: includes traditional Oriental preserved products, such as salt-cured duck eggs and alkaline treated ‘thousand-year-old-eggs’. Egg-based desserts: includes ready-to-eat products and products to be prepared from a dry mix. Examples include: flan and egg custard. This also includes custard fillings for fine bakery wares (e.g. pies). Eggs and egg products ZOO_CAT_FOODVH B09647B Eggs and egg products Bovine meat is defined as edible parts of domestic bovine animals (including Bubalus and Bison species), including blood (Regulation (EC) No 853\/2004). Please also note the following related definitions in the EU legislation, which can help to specify the foodstuff implicated in the free text data element. Fresh meat is meat that has not undergone any preserving process other than chilling, freezing or quick-freezing, including meat that is vacuum-wrapped or wrapped in a controlled atmosphere (Regulation (EC) No 853\/2004). Meat preparations are defined as fresh meat, including meat that has been reduced to fragments, which has had foodstuffs, seasonings or additives added to it or which has undergone processes insufficient to modify the internal muscle fibre structure of the meat and thus to eliminate the characteristics of fresh meat (Regulation (EC) No 853\/2004). Minced meat is boned meat that has been minced into fragments and contains less than 1 % salt (Regulation (EC) No 853\/2004), for example steak tartare. Meat products are defined as processed products resulting from the processing of meat or from further processing of such processed products, so that the cut surface shows that the product no longer has the characteristics of fresh meat (Regulation (EC) No 853\/2004). Examples of bovine meat and products thereof include: beef steak, stewing steak, grilled liver, roast beef, sausages and steak tartare. Bovine meat and products thereof ZOO_CAT_FOODVH B09667B Bovine meat and products thereof Pig meat is defined as edible parts of domestic porcine animals, including blood (Regulation (EC) No 853\/2004). For the definition of meat products please see ‘Bovine meat and products thereof’. Pig meat and products thereof ZOO_CAT_FOODVH B09687B Pig meat and products thereof Sheep meat is defined as edible parts of domestic ovine animals, including blood (Regulation (EC) No 853\/2004). Sheep meat and products thereof ZOO_CAT_FOODVH B09707B Sheep meat and products thereof Other red meat is meat from species, other than birds, that are not mentioned above, such as wild game and farmed game. Wild game includes wild ungulates and lagomorphs, as well as other land mammals that are hunted for human consumption. Meat from wild boars is classified in this category; it would be desirable to indicate in the comment section that the mean pertains to wild boar.Farmed game includes farmed ratites and farmed land mammals other than those referred to as ‘Domestic ungulates’ (Regulation (EC) No 853\/2004).Mixed red meat is a mix of red meat from different species, e.g. meatballs consisting of bovine and pig meat.For the definition of meat products please see ‘Bovine meat and products thereof’. Other or mixed red meat and products thereof ZOO_CAT_FOODVH B09727B Other or mixed red meat and products thereof Broiler meat is defined as edible parts of domestic chicken (Gallus gallus), including blood.For the definition of meat products please see ‘Bovine meat and products thereof’. Broiler meat (Gallus gallus) and products thereof ZOO_CAT_FOODVH B09747B Broiler meat (Gallus gallus) and products thereof Turkey meat is defined as edible parts of domestic turkeys, including blood. For the definition of meat products please see ‘Bovine meat and products thereof’. Turkey meat and products thereof ZOO_CAT_FOODVH B09767B Turkey meat and products thereof Other poultry meat is defined as edible parts of ‘poultry’, including blood. ‘Poultry’ are farmed birds, including birds that are not considered as domestic but which are farmed as domestic animals, with the exception of ratites, which are considered ‘farmed game’ (Regulation (EC) No 853\/2004). In this case, all poultry EXCEPT Gallus and turkey. Examples in this category include duck, goose, pheasant, guinea fowl and ostrich. For the definition of meat products please see ‘Bovine meat and products thereof’. Other, mixed or unspecified poultry meat and products thereof ZOO_CAT_FOODVH B09787B Other, mixed or unspecified poultry meat and products thereof Fish, as a food, describes the edible parts of water-dwelling, cold-blooded vertebrates with gills. Examples of edible fish include salmon, trout, tuna, eel, silver carp and anchovy. Examples of fish products include frozen fish fingers, roe and smoked salmon. Please specify the fish species (e.g. salmon, herring) as well as the treatment (e.g. smoked, raw, cooked) in the free text data element (for example: ‘cold-smoked salmon’). Fish and fish products ZOO_CAT_FOODVH B09807B Fish and fish products Shellfish is a broad term for all aquatic animals that have a shell of some kind. Shellfish are separated into two basic categories: crustaceans and molluscs. However, the EU definition of shellfish includes only bivalve and gastropod molluscs (Council Directive 79\/923\/EEC). Examples of edible shellfish are sea cucumber and sea urchin. Crustaceans are one of two main classifications of shellfish (the other being mollusc). Crustaceans have elongated bodies and jointed, soft (crust-like) shells. Examples of edible crustaceans include shrimp (e.g. Atlantic white shrimp), prawn (e.g. giant river prawn), lobster (e.g. European lobster), crayfish (e.g. European crayfish) and crab (e.g. edible crab). Molluscs are animals with a soft body, internal or external shell, muscular foot and\/or tentacles. Molluscs are divided into three groups: gastropods (also called univalves), bivalves (including live bivalve molluscs) and cephalopods. Examples of edible molluscs include abalone (sea ear), snail (e.g. vineyard snail) and clam.Examples of edible bivalve molluscs include mussels and oysters. Please specify the species as well as the treatment (e.g. live, cooked) in the free text data element (for example: ‘deep-fried shrimps’). Crustaceans, shellfish, molluscs and products thereof ZOO_CAT_FOODVH B09827B Crustaceans, shellfish, molluscs and products thereof Vegetables are plants or parts of plants cultivated for food. Some foods that are botanically fruits, such as tomatoes and cucumbers, and seeds, such as peas and beans, are included with the vegetables; some plants, such as rhubarb, are classed as fruit, although they are not botanically fruits. The distinction in popular usage depends on whether they are eaten as savoury (vegetables) or sweet (fruit) dishes. Examples of vegetables include cauliflower, broccoli, pea, cucumber, lentil, avocado and garlic. ‘Sea vegetables’ like sea lettuce and seaweed are also part of this group. Vegetable juice is the juice obtained from vegetables and usually made from carrots, beets, pumpkin or tomatoes. Please specify the plant species or cultivar group as well as the treatment (e.g. raw, cooked juice) in the free text data element (for example: ‘raw iceberg lettuce’). Vegetables and juices and other products thereof ZOO_CAT_FOODVH B09847B Vegetables and juices and other products thereof Food preserved by canning; the process of preserving food by sterilisation and cooking in a sealed metal can, which destroys bacteria and protects against recontamination.Please specify the canned food product (e.g. meat, fish, vegetable) in the free text data element (for example: ‘baked beans, canned’). Canned food products ZOO_CAT_FOODVH B09867B Canned food products Cereal is grass whose starchy grains are used as food, for example wheat, rice, rye, oats, maize, buckwheat, millet and grain. Foodstuff prepared from the starchy grains of cereal grasses is also referred to as cereal. Please specify the cereal products (e.g. plant species) and treatment (cut, precut, cooked) in the free text data element. Cereal products including rice and seeds/pulses (nuts, almonds) ZOO_CAT_FOODVH B09887B Cereal products including rice and seeds/pulses (nuts, almonds) Fruit is defined as all fruit. Tomatoes are not regarded as fruit (Council Directive 2001\/112\/EC ). Fruit purée is defined as the fermentable but unfermented product obtained by sieving the edible part of whole or peeled fruit without removing the juice (Council Directive 2001\/112\/EC). Fruit juice is defined as:The fermentable but unfermented product obtained from fruit which is sound and ripe, fresh or preserved by chilling, of one or more kinds mixed together, having the characteristic colour, flavour and taste typical of the juice of the fruit from which it comes. Flavour, pulp and cells from the juice which are separated during processing may be restored to the same juice. In the case of citrus fruits, the fruit juice must come from the endocarp. Lime juice, however, may be obtained from the whole fruit, by suitable production processes whereby the proportion of constituents of the outer part of the fruit is reduced to a minimum.The product obtained from concentrated fruit juice by: – replacing, in the concentrated fruit juice, water extracted from that juice during concentration, restoring the flavours and, if appropriate, pulp and cells lost from the juice but recovered during the process of producing the fruit juice in question or of fruit juice of the same kind. The water added must display appropriate characteristics, particularly from the chemical, microbiological and organoleptic viewpoints, in such a way as to guarantee the essential qualities of the juice. The product thus obtained must display organoleptic and analytical characteristics at least equivalent to those of an average type of juice obtained from fruits of the same kind within the meaning of (a) (Council Directive 2001\/112\/EC). Concentrated fruit juice is the product obtained from fruit juice of one or more kinds by the physical removal of a specific proportion of the water content. Where the product is intended for direct consumption that removal will be of at least 50% (Council Directive 2001\/112\/EC). Fruit nectar is the fermentable but unfermented product obtained by adding water and sugars and\/or honey to the products to fruit purée or to a mixture of those products, that, moreover, meet the requirements of Annex IV (Council Directive 2001\/112\/EC). Fruit, berries and juices and other products thereof ZOO_CAT_FOODVH B09907B Fruit, berries and juices and other products thereof Drinks are any liquids suitable for drinking, also called beverages.Juice drinks are drinks made from fruit juice plus other ingredients, such as water, flavourings, artificial sweeteners, colourings and preservatives. Fruit juice drink can contain as little as 5% juice. Soft drinks are non-alcoholic, flavoured, carbonated beverages, usually commercially prepared and sold in bottles or cans. Alcoholic drinks are made by fermenting fruit juices, sugars and fermentable carbohydrates with yeast to form alcohol. These include beer, cider and perry, 4–6% alcohol by volume; wines, 9–13% alcohol; spirits (e.g. brandy, gin, rum, vodka, whisky) made by distilling fermented liquor, 38–45% alcohol; liqueurs made from distilled spirits, sweetened and flavoured, 20–40% alcohol; and fortified wines (aperitif wines, Madeira, port, sherry) made by adding spirit to wine, 18–25% alcohol. In the context of the food-borne outbreak system the category ‘Drinks, including bottled water’ does not include milk, fruit juice, fruit nectar, vegetable juice and tap water, but it includes fruit-flavoured drinks and juice drinks. The definition of drinks also includes hot drinks such as coffee and tea. Bottled water is sold for human consumption. It is sealed in a sanitary container and must meet all regulations for drinking water. Bottled water contains no sweeteners or chemical additives and must be calorie and sugar-free. ‘Natural mineral water’ means microbiologically wholesome water originating in an underground water table or deposit and emerging from a spring tapped at one or more natural or bore exits. Before water is recognised as a natural mineral water, it has to be demonstrated that it: is obtained from an underground source, has a stable composition, is protected from all sources of pollution, meets chemical and microbiological safety standards, is not subject to treatment which affects its characteristic properties. Natural mineral water is bottled at source and is sold under one trade description. The name of the source and its place of exploitation are stated on the label together with a statement of the analytical composition (EC Directives 80\/777, 96\/70 and 80\/778).In contrast, recognition of a spring water underground source is not required. Spring water meets the same chemical and microbiological standards as tap water and, currently, can be subject to treatment. However, like natural mineral water, spring water is bottled at source, sold under one trade description and the name of the source and its place of exploitation are included in labelling (EC Directives 80\/777, 96\/70 and 80\/778). Bottled drinking water, which is not restricted to a particular type of source, comprises bottled water, other than natural mineral water and spring water, and includes water referred to as ‘table water’. Bottled drinking water is required to comply with the same compositional and microbiological standards as tap water (EC Directives 80\/777, 96\/70 and 80\/778). Drinks, including bottled water ZOO_CAT_FOODVH B09927B Drinks, including bottled water Tap water or ordinary drinking water refers to: all water, either in its original state or after treatment, intended for drinking, cooking, food preparation or other domestic purposes, regardless of its origin and whether it is supplied from a distribution network, from a tanker or in bottles or containers (Council Directive 98\/83\/EC). In this context, tap water, including well-water, does not include water in bottles. Water in bottles is included in the item ‘Drinks, including bottled water’. Please specify in the free text data element whether the water was treated or untreated. Tap water, including well water ZOO_CAT_FOODVH B09947B Tap water, including well water Sweets are foods, such as candy, milk-free puddings or preserves, which are high in sugar content and milk-free puddings. Candy, specifically sugar candy, is a confection made from a concentrated solution of sugar in water, to which a variety of flavourings and colorants is added. Some candy, like marshmallows and gummy bears, may contain gelatine. Preserves refer to fruit, or vegetables, that have been prepared, canned or jarred for long-term storage. Examples for preserves are jam and jelly. Chocolate is obtained by an adequate manufacturing process from cocoa materials which may be combined with milk products, sugars and\/or sweeteners and other additives. Other edible foodstuffs, excluding added flour and starch and animal fats other than milk fat, may be added to form various chocolate products (Directive 2000\/36\/EC ). Sweets and chocolate ZOO_CAT_FOODVH B09967B Sweets and chocolate Bakery products includes bread and ordinary bakery wares (all types of non-sweet bakery products and bread-derived products) and sweet, salty and savoury fine bakery wares (ready-to-eat products as well as mixes for preparing fine baked goods). Bread and ordinary bakery wares: The category bread contains the main sub-categories white bread, brown bread and wholemeal bread. Crackers, excluding sweet crackers: the term ‘cracker’ refers to a thin, crisp wafer, usually of unsweetened dough. Flavoured crackers (e.g. cheese flavoured). Examples include: soda crackers, rye crisps and matzahs. Other ordinary bakery products: includes all other ordinary bakery wares, such as bagels, pita, English muffins, cornbread and biscuits. The term ‘biscuit’ in this category refers to a small cake of shortened bread, leavened with baking powder or baking soda. It does not refer to the British ‘biscuit,’ which is a ‘cookie’ or ‘sweet cracker’ included in the category Cakes, cookies and pies. Bread-type products, including bread stuffing and bread crumbs: includes bread-based products, such as croutons, bread stuffing and stuffing mixes and prepared doughs (e.g. for biscuits). Fine bakery wares (sweet, salty and savoury) and mixes: Cakes, cookies and pies (e.g. fruit-filled or custard types): the term ‘sweet cracker’ or ‘sweet biscuit’ used in this category refers to a cookie-like product that may be eaten as a dessert. Examples include: butter cake, cheesecake, fruit-filled cereal bars, pound cake, moist cake, western cakes, moon cakes, sponge cake, fruit-filled pies (e.g. apple pie), oatmeal cookies, sugar cookies and British ‘biscuits’ (cookies or sweet crackers). Other fine bakery products: includes products that may be eaten as a dessert or as breakfast. Examples include: doughnuts, sweet rolls, scones, muffins, pancakes, waffles, filled sweet buns, Danish pastries, wafers or cones for ice cream, flour confectionery and trifles. This category also includes tiramisu. Please specify the sub-category (e.g. fine bakery wares, pies) and, if available, the filling (e.g. fruit, custard, raw eggs) in the free text data element (for example: ‘fine bakery product containing pasteurised dairy products and raw eggs, tiramisu’). Bakery products ZOO_CAT_FOODVH B09987B Bakery products Herbs are the aromatic leaves of plants without woody stems that grow in temperate zones. Spices are seasonings obtained from the bark, buds, fruit or flower parts, roots, seeds or stems of various aromatic plants and trees. Herbs and spices are usually derived from botanical sources, which may be dehydrated and are either ground or whole. Examples of herbs include basil, oregano and thyme. Examples of spices include cumin and caraway seeds. Spices may also be found as blends in powder or paste form. Examples of spice blends include chilli seasoning, chilli paste, curry paste, curry roux and dry cures or rubs that are applied to external surfaces of meat or fish. Herbs and spices ZOO_CAT_FOODVH B10007B Herbs and spices This category should be chosen if the implicated food is none of those mentioned above. In this case, it should be specified in the free text data element. Other foods ZOO_CAT_FOODVH B10047B Other foods Mixed meals are meals composed of various foods, for example paella, risotto, curries and nasi goreng. This category also includes miscellaneous foodstuffs served on one plate. Please also select this category if it was not possible to narrow the suspected food down to an individual food or ingredient during the investigation of the food-borne outbreak. Mixed food ZOO_CAT_FOODVH B29387B Mixed food A buffet meal is a meal at which guests serve themselves from various dishes displayed on a large table. Buffet meals ZOO_CAT_FOODVH B29407B Buffet meals General outbreak: outbreak involving human cases from more than one household. Outbreaks in residential homes (e.g. nursing homes), schools and other similar institutions are considered to be general outbreaks. General ZOO_CAT_OUTBRK TB01A General Household outbreak: outbreak where all the human cases live in one single household. Household ZOO_CAT_OUTBRK TB02A Household / domestic kitchen Unknown Unknown ZOO_CAT_OUTBRK TB03A Unknown animal sample ZOO_CAT_SMPTYP S000A animal sample animal sample - blood ZOO_CAT_SMPTYP S001A animal sample - blood animal sample - caecum ZOO_CAT_SMPTYP S002A animal sample - caecum animal sample - ear ZOO_CAT_SMPTYP S003A animal sample - ear animal sample - eggs ZOO_CAT_SMPTYP S004A animal sample - eggs animal sample - faeces ZOO_CAT_SMPTYP S005A animal sample - faeces animal sample - fleece ZOO_CAT_SMPTYP S006A animal sample - fleece animal sample - foetus/stillbirth ZOO_CAT_SMPTYP S007A animal sample - foetus/stillbirth animal sample - lymph nodes ZOO_CAT_SMPTYP S008A animal sample - lymph nodes animal sample - meat juice ZOO_CAT_SMPTYP S009A animal sample - meat juice animal sample - milk ZOO_CAT_SMPTYP S010A animal sample - milk animal sample - rectum-anal swab ZOO_CAT_SMPTYP S012A animal sample - rectum-anal swab animal sample - vaginal swab ZOO_CAT_SMPTYP S013A animal sample - vaginal swab animal sample - placental swab ZOO_CAT_SMPTYP S014A animal sample - placental swab animal sample - nasal swab ZOO_CAT_SMPTYP S015A animal sample - nasal swab animal sample - organ/tissue ZOO_CAT_SMPTYP S017A animal sample - organ/tissue animal sample - tonsil ZOO_CAT_SMPTYP S018A animal sample - tonsil food sample ZOO_CAT_SMPTYP S019A food sample food sample - blood ZOO_CAT_SMPTYP S020A food sample - blood food sample - carcase swabs ZOO_CAT_SMPTYP S021A food sample - carcase swabs food sample - meat ZOO_CAT_SMPTYP S022A food sample - meat food sample - milk ZOO_CAT_SMPTYP S023A food sample - milk food sample - neck skin ZOO_CAT_SMPTYP S024A food sample - neck skin food sample - tonsil ZOO_CAT_SMPTYP S025A food sample - tonsil feed sample ZOO_CAT_SMPTYP S026A feed sample environmental sample ZOO_CAT_SMPTYP S027A environmental sample environmental sample - boot swabs ZOO_CAT_SMPTYP S028A environmental sample - boot swabs environmental sample - dust ZOO_CAT_SMPTYP S029A environmental sample - dust unknown ZOO_CAT_SMPTYP S030A unknown animal sample - cloacal swab ZOO_CAT_SMPTYP S031A animal sample - cloacal swab animal sample - eggshells ZOO_CAT_SMPTYP S032A animal sample - eggshells environmental sample - air ZOO_CAT_SMPTYP S033A environmental sample - air environmental sample - fabric swab ZOO_CAT_SMPTYP S034A environmental sample - fabric swab environmental sample - hatcher basket liner ZOO_CAT_SMPTYP S035A environmental sample - hatcher basket liner animal sample - brain ZOO_CAT_SMPTYP S036A animal sample - brain environmental sample - delivery box liner ZOO_CAT_SMPTYP S037A environmental sample - delivery box liner animal sample - hide ZOO_CAT_SMPTYP S038A animal sample - hide environmental sample - boot swabs and dust ZOO_CAT_SMPTYP S039A environmental sample - boot swabs and dust Person:Alan Ruttenberg has part my body has part my brain (continuant parthood, two material entities) my stomach has part my stomach cavity (continuant parthood, material entity has part immaterial entity) this year has part this day (occurrent parthood) a core relation that holds between a whole and its part Everything has itself as a part. Any part of any part of a thing is itself part of that thing. Two distinct things cannot have each other as a part. Occurrents are not subject to change and so parthood between occurrents holds for all the times that the part exists. Many continuants are subject to change, so parthood between continuants will only hold at certain times, but this is difficult to specify in OWL. See https://code.google.com/p/obo-relations/wiki/ROAndTime Parthood requires the part and the whole to have compatible classes: only an occurrent have an occurrent as part; only a process can have a process as part; only a continuant can have a continuant as part; only an independent continuant can have an independent continuant as part; only a specifically dependent continuant can have a specifically dependent continuant as part; only a generically dependent continuant can have a generically dependent continuant as part. (This list is not exhaustive.) A continuant cannot have an occurrent as part: use 'participates in'. An occurrent cannot have a continuant as part: use 'has participant'. An immaterial entity cannot have a material entity as part: use 'location of'. An independent continuant cannot have a specifically dependent continuant as part: use 'bearer of'. A specifically dependent continuant cannot have an independent continuant as part: use 'inheres in'. has_part BFO:0000051 uberon has_part has_part has part has part To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) To say that each spatiotemporal region s temporally_projects_onto some temporal region t is to say that t is the temporal extension of s. (axiom label in BFO2 Reference: [080-003]) To say that spatiotemporal region s spatially_projects_onto spatial region r at t is to say that r is the spatial extent of s at t. (axiom label in BFO2 Reference: [081-003]) X in_left_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the left portion. BSPO:0000120 uberon in_left_side_of in_left_side_of in_left_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X in_right_side_of Y <=> if Y is subdivided into left and right portions, X is part_of the right portion. BSPO:0000121 uberon in_right_side_of in_right_side_of in_right_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X anterior_side_of Y <=> if Y is subdivided into two anterior and posterior portions, X is part_of the anterior portion. BSPO:0000123 uberon in_anterior_side_of in_anterior_side_of in_anterior_side_of X in_lateral_side_of Y <=> if X is in_left_side_of Y or X is in_right_side_of Y. X is often, but not always a paired structure BSPO:0000126 uberon in_lateral_side_of in_lateral_side_of in_lateral_side_of https://github.com/obophenotype/uberon/wiki/Modeling-paired-structures-Design-Pattern X proximalmost_part_of Y <=> X is part_of Y and X is adjacent_to the proximal boundary of Y BSPO:0001106 uberon proximalmost_part_of proximalmost_part_of proximalmost_part_of X distalmost_part_of Y <=> X is part_of Y and X is adjacent_to the distal boundary of Y BSPO:0001108 uberon distalmost_part_of distalmost_part_of distalmost_part_of This document is about information artifacts and their representations is_about is a (currently) primitive relation that relates an information artifact to an entity. 7/6/2009 Alan Ruttenberg. Following discussion with Jonathan Rees, and introduction of "mentions" relation. Weaken the is_about relationship to be primitive. We will try to build it back up by elaborating the various subproperties that are more precisely defined. Some currently missing phenomena that should be considered "about" are predications - "The only person who knows the answer is sitting beside me" , Allegory, Satire, and other literary forms that can be topical without explicitly mentioning the topic. person:Alan Ruttenberg Smith, Ceusters, Ruttenberg, 2000 years of philosophy is about has material basis in The relation between the conclusion "Gene tpbA is involved in EPS production" and the data items produced using two sets of organisms, one being a tpbA knockout, the other being tpbA wildtype tested in polysacharide production assays and analyzed using an ANOVA. The relation between a data item and a conclusion where the conclusion is the output of a data interpreting process and the data item is used as an input to that process OBI OBI Philly 2011 workshop is_supported_by_data has_specified_input has_specified_input see is_input_of example_of_usage A relation between a planned process and a continuant participating in that process that is not created during the process. The presence of the continuant during the process is explicitly specified in the plan specification which the process realizes the concretization of. 8/17/09: specified inputs of one process are not necessarily specified inputs of a larger process that it is part of. This is in contrast to how 'has participant' works. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Coutot has_specified_input has_specified_output has_specified_output A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. PERSON: Alan Ruttenberg PERSON: Bjoern Peters PERSON: Larry Hunter PERSON: Melanie Courtot has_specified_output is_specified_output_of is_specified_output_of A relation between a planned process and a continuant participating in that process. The presence of the continuant at the end of the process is explicitly specified in the objective specification which the process realizes the concretization of. Alan Ruttenberg PERSON:Bjoern Peters is_specified_output_of a relation between two independent continuants, the target and the location, in which the target is entirely within the location RO:0001025 uberon RO:0001025 located_in located_in located in located_in RO:0002007 uberon bounding_layer_of bounding_layer_of A relationship that applies between a continuant and its outer, bounding layer. Examples include the relationship between a multicellular organism and its integument, between an animal cell and its plasma membrane, and between a membrane bound organelle and its outer/bounding membrane. bounding layer of RO:0002351 uberon has_member has_member has member RO:0002433 uberon contributes_to_morphology_of contributes_to_morphology_of contributes to morphology of x composed_primarily_of y iff: more than half of the mass of x is made from parts of y RO:0002473 uberon composed_primarily_of composed_primarily_of composed primarily of RO:0002494 transforms from uberon transformation_of transformation_of transformation of RO:0003000 uberon produces produces produces RO:0003001 uberon produced_by produced_by produced_by Crawford Revie Eva Blomqvist Karl Hammar Matthias Filter Patrick Lambrix Taras Günther Fernanda Dórea An ontology to support semantic interoperability among domains involved in health surveillance (animal health, public health and food safety). More details at http://datadrivensurveillance.org. Health Surveillance Ontology (HSO) This is an ontology to support (one) health surveillance, focused on "surveillance system level data", that is, data outputs from surveillance activities, such as number of samples collected, cases observed, etc. x is a conduit for y iff y passes through the lumen of x. uberon conduit_for conduit for uberon protects protects