http://klarman.synthasite.com/ http://www.brunel.ac.uk/people/larisa-soldatova Probabilistic Knowledge Assembly (PANDA) Ontology has been developed in the context of the DARPA's Big Mechanism research program. It provides a semantic interface for capturing information on molecular interactions extracted from scientific texts. Conceptually, PAF ontology supports 3 layers of representation: 1) Domain knowledge: molecular interactions, their participants, structure, and (possibly) formal relationships to some external biological models. 2) Textual evidence: sentences extracted from text, speaking about those interactions, and their provenance-related information. 3) Probabilisitic information associated with different aspects of the representation (see the imported Uncertainty Ontology). biological events molecular biology text mining Probabilistic Knowledge Assembly Ontology 0.9 has definition a statment is contained in an index card contained in An index card contains a statement contains statement contradicts corroborates Scientific evidence supporting the existence of the entity as described. evidence extends an index card has an annotator (computer+machine, human, or both) has annotator The relationship between oa:Annotation and body. The body is somehow "about" the oa:hasTarget of the annotation. The Body may be of any media type, and contain any type of content. The Body SHOULD be identified by HTTP URIs unless they are embedded within the Annotation. Embedded bodies SHOULD be instances of cnt:ContentAsText and embed their content with cnt:chars. They SHOULD declare their media type with dc:format, and MAY indicate their language using dc:language and a RFC-3066 language tag. There is no OA class provided for "Body" as a body might be a target of a different annotation. However, there SHOULD be 1 or more content-based classes associated with the body resources of an Annotation, and the dctypes: vocabulary is recommended for this purpose, for instance dctypes:Text to declare textual content. has body Statements qualify the truth of biological events in the context of certain cell types. Hence a statment should be by defeault connected to some cell type via "has cell type" property. has cell type Statements qualify the truth of biological events in the context of certain cell lines. Hence a statment should be by defeault connected to some cell line via "has cell line" property. has cell line Complex chemicals conist of (simple) components. has component values accepted (by DARPA) protein modification; binding; mutation should be attached to a chemical entity - a participant of an event has feature A molecular interaction of type adds_modification or inhibits_modification should by default have some modification feature of type protein modification. has modification feature OBI, IAO has participant has participant A has participant B An event has been evaluated in a wet lab experiment, whose results are reported has related experimental results has submitter The relationship between oa:Annotation and target. The target resource is what the oa:hasBody is somewhat "about". The target may be of any media type, and contain any type of content. The target SHOULD be identified by HTTP URIs unless they are embedded within the Annotation. Embedded targets SHOULD be instances of cnt:ContentAsText and embed their content with cnt:chars. They SHOULD declare their media type with dc:format, and MAY indicate their language using dc:language and a RFC-3066 language tag. There is no OA class provided for "Target" as a target might be a body in a different annotation. However, there SHOULD be 1 or more content-based classes associated with the target resources of an Annotation, and the dctypes: vocabulary is recommended for this purpose, for instance dctypes:Text to declare textual content. has target Statements qualify the truth of biological events in the context of certain tissue types. Hence a statment should be by defeault connected to some tissue type via "has tissue type" property. has tissue type Statements qualify the truth of biological events in the context of certain organisms. Hence a statment should be by defeault connected to some organism via "in organism" property. in organism is_about is a (currently) primitive relation that relates an information artifact to an entity. http://purl.obolibrary.org/obo/IAO_0000136 is about a statement is extracted from an article is extracted from an event is represented by a statement is represented by a core relation that holds between a part and its whole part of The nodes of petri net models are labeled with biological entities: places with chemicals or interactions, while transitions with regulation types (classes). has petri net label A journal article is published in a journal published in relation to model a statement represents an event represents specifies The transitions in petri net models follow the direction: 'transition from' a place; 'transition to' a place. transition from The transitions in petri net models follow the direction: 'transition from' a place; 'transition to' a place. transition to associates an identifier with a chemical entity, e.g.: GAB1_HUMAN, MK03_HUMAN has entity ID entity's name as accepted in one of the official databases has entity name associates a chemical entity with its textual representation in the extracted text fragment has entity text a journal has an H index has H-index has ISSN has index card ID has PMC ID a publication has publication year has publication year https://en.wikipedia.org/wiki/SCImago_Journal_Rank A journal has its SJR score has SJR score Certain interactions, e.g. modificiations or bindings, are additionally qualified by the site (by default of the participant B) where the interaction takes palce. has site has start time has stop time a submitter has an id has submitter ID has textual evidence A journal/publication has title. has title - a statement states the truth value of an event - an experimental result states the truth value of the tested hypothesis Values: true/false has truth value panda:Abstract A summary of the entire document that is substantially smaller than the document it summarizes. It is about the document it summarizes. abstract panda:Acetylation MI:0192 acetylation panda:AddsModification adds modification panda:Annotation Typically an Annotation has a single Body (oa:hasBody), which is the comment or other descriptive resource, and a single Target (oa:hasTarget) that the Body is somehow "about". The Body provides the information which is annotating the Target. This "aboutness" may be further clarified or extended to notions such as classifying or identifying with oa:motivatedBy. annotation panda:Annotator The agent that provided an annotation (extracted a sentence). annotator panda:Binding The selective, non-covalent, often stoichiometric, interaction of a molecule with one or more specific sites on another molecule. binding panda:Cell cell panda:CellLine cell line panda:Chemical chemical panda:ChemicalFamily chemical family panda:Complex complex panda:Computer computer panda:Database database panda:Deacetylation MI:0197 deacetylation panda:DecreasesActivity decreases activity panda:Defarnesylation MI:0198 defarnesylation panda:Deglycosylation MI:0558 deglycosylation panda:Demethylation MI:0871 demethylation panda:Dephosphorylation MI:0203 dephosphorylation panda:Desumoylation MI:0568 desumoylation panda:Deubiquitination MI:0204 deubiquitination panda:DiscussionSectionOfaPublication A part of a publication about an investigation that is about the study interpretation of the investigation discussion section of a publication panda:Document A collection of information content entities intended to be understood together as a whole document panda:DocumentPart an information content entity that is part of a document document part panda:Event A biological event, such as molecular interaction or gene expression. Events are desccribed in statements. biological event panda:ExperimentalResults Experimental results are the set of facts and conclusions, obtained as a result of the interpretation of the experimental observations, which increase/decrease the probability of a research hypothesis of the experiment. experimental results panda:Farnesylation MI:0206 farnesylation panda:FigureLegend A legend associated with a figure in a document figure legend panda:Gene gene panda:GeneExpression The process in which a gene's sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA (for protein-coding genes) and the translation of that mRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form. http://purl.obolibrary.org/obo/GO_0010467 gene expression panda:Glycosylation MI:0559 glycosylation panda:Human human panda:HumanComputer human with computer panda:Hydroxylation MI:0210 hydroxylation panda:IncreasesActivity increases activity panda:IndexCard index card panda:InhibitsModification inhibits modification panda:IntroductionToaPublication A part of a publication about an investigation that is about the objective specification (why the investigation is being done) introduction to a publication panda:Journal journal panda:JournalArticle a report that is published in a journal journal article panda:MethodsSection A part of a publication about an investigation that is about the study design of the investigation methods section panda:Methylation MI:0213 methylation panda:Model defined by BioModels ontology http://bioonto.de/ro2.owl#Model model panda:ModelComponent defined by BioModels ontology model component panda:MolecularInteraction An interaction in which participants bind physically to each other, directly or indirectly through intermediary molecules. Rationale: There is a large body of interaction data, mostly produced by high throughput systems, that does not satisfy the level of detail required to model them with ComplexAssembly class. Specifically, what is lacking is the stoichiometric information and completeness (closed-world) of participants required to model them as chemical processes. Nevertheless interaction data is extremely useful and can be captured in BioPAX using this class. Usage: This class should be used by default for representing molecular interactions such as those defined by PSI-MI level 2.5. The participants in a molecular interaction should be listed in the PARTICIPANT slot. Note that this is one of the few cases in which the PARTICPANT slot should be directly populated with instances (see comments on the PARTICPANTS property in the interaction class description). If all participants are known with exact stoichiometry, ComplexAssembly class should be used instead. Example: Two proteins observed to interact in a yeast-two-hybrid experiment where there is not enough experimental evidence to suggest that the proteins are forming a complex by themselves without any indirect involvement of other proteins. This is the case for most large-scale yeast two-hybrid screens. BioPax level3; 2 molecular interaction panda:Mutation mutation panda:NegativeRegulation decreases GENIA negative regulation panda:Organism organism panda:Paragraph A paragraph in a document paragraph panda:Participant Refers to the material entities participating in a biological event participant panda:PetriNetModel petri net model panda:PetriNetModelComponent petri net model component panda:Phosphorylation MI:0217 phosphorylation 1 panda:Place place panda:PositiveRegulation increases positive regulation panda:Protein protein panda:ProteinFamily protein family panda:ProteinModification BEL, GRO protein modification panda:Publication A document that has been accepted by a publisher publication panda:Regulation BEL, BioPax , level 3?, GO: biological regulation regulation panda:ResultsSection A part of a publication about an investigation that is about a study design execution results section panda:Ribosylation GO ribosylation panda:Statement statement panda:Submitter The agent that submitted the annotation to the system. submitter panda:Sumoylation MI:0566 sumoylation panda:Table table panda:TextualEntity A textual entity is a part of a manifestation (FRBR sense), a generically dependent continuant whose concretizations are patterns of glyphs intended to be interpreted as words, formulas, etc. textual entity panda:Tissue tissue 1 1 1 panda:Transition transition panda:Translocation MI parent class: cross-reference type? MI:0593 translocation panda:Ubiquitination MI:0220 ubiquitination BFO:0000023 BFO:0000040 IAO:0000030 owl:Thing entity 0.9 http://klarman.synthasite.com/ http://www.brunel.ac.uk/people/larisa-soldatova Probabilistic Knowledge Assembly (PANDA) Ontology has been developed in the context of the DARPA's Big Mechanism research program. It provides a semantic interface for capturing information on molecular interactions extracted from scientific texts. Conceptually, PAF ontology supports 3 layers of representation: 1) Domain knowledge: molecular interactions, their participants, structure, and (possibly) formal relationships to some external biological models. 2) Textual evidence: sentences extracted from text, speaking about those interactions, and their provenance-related information. 3) Probabilisitic information associated with different aspects of the representation (see the imported Uncertainty Ontology). biological events molecular biology text mining Probabilistic Knowledge Assembly Ontology 0.9