The GBOL API code generated from the GBOL owl file GBOL Api life.gbol.GBOLApi GBOLApi 0.1 PCR_primers The type of QTL The base after which the in between two bases location is located Alternative Organism The encoded amino acid Note on the provenance All annotation result within the GBOL data set The position of the anticodon within the tRNA transcript anticodon The anti codon of the TRNA linked to tRNA which points to a AntiCodon object artificial_location Indicate that the location is artificial because of a heterogeneous population for low quality sequence region Indicate that a feature has a artificial location with reason, added to feature, was originally only possible for mRNA and CDS to fix frame-shifts key:mRNA, CDS The optional assembly information of the sequence Taxonomy associated markers linked to the QTL region ASV sequence set ASV assignment The position of the base Barcode sequence set The begin position comes always first then the the end position. So for a gene on the reverse complementary strain the begin position is equal to the stop position. We use the same positioning definition as in GenBank and Faldo. If known, a region within another protein that binds this region. If region of other protein is unknown use fuzzy position from begin to end. SignalP properties Any publication associated to feature annotation Replaced in GBOl to citation reference in both the feature and Sequence Object collected_by The persons or institute who collected the specimen Type of the collection sample Optional list of entities that are contained within the file country The country Link to the other cross link The database to with the links link to Cross references to other databases containing the same record Optionally give a list of features upon which it is based Option to denote the type of domain The begin position comes always first then the the end position. So for a gene on the reverse complementary strain the begin position is equal to the stop position. We use the same positioning definition as in GenBank and Faldo. The type of this GBOLDataSet The position of region which translate to other amino acid then the default translation table All exons that are part of the gene This list off exons that form this transcript, in case of prokaryote it contains one element To which experiment this expression value belongs to Replaced with the provenance infrastructure, use the onProperty property to denote to which property it relates Expression feature Expression type The set of features annotating the sequence Optionally set the fileType The forward primer(s) The forward primer(s) The forward primer(s) gap_type The type of the gap Added to the Gap class Genotypes of the sample the variant was called on The geographical coordinates(latitude + longitude) of the location where the specimen was collected The geographical location(country or ocean) from which the sample is collected host The host of the organism (from which the sample was obtained), which it lives in, upon or attached to in its natural environment. identified_by The name of the expert who identified the specimen taxonomically The type of the immunoglobulin region The included region of referenced sequence, only exact position must be used to denote the start en end region, reference property should be empty. Use the strand property to include forward or reverse complement strand. Reference to the sequence that is included The xref from which the sequence is included Read data used as input If this NA object is integrated into another NA object, for example a phage genome which is integrated into a bacterial genome or a plasmid which is integrated into a yeast genome. The region of the virus genome that is integrated All introns that are part of the gene linkage_evidence The linkage evidence use to link the sequences on both sides add to the Gap feature class, enumeration created All databases that are linked by any of the contained XRefs TMHMM properties A set of regions making up a location spreader over multiple regions. The members inherit the reference value from this CollectionOfRegions object. mobile_element_type Mobile element type replaced with mobileElementType and mobileElement properties mod_base The type of modification Enumeration type added, property is in modified base feature ncRNA_class The type of the non coding RNA enum added to ncRNA note A set off some additional notes Each feature can have note The name of the ocean operon Operon to which the genetic element belongs to Link to operon added in genomic feature The organism from which the sequence originates from All associated organisms Link to the data-wise provenance Parental strains The resulting product protein when translating this CDS, each protein should have an IRI equal to http://gbol.life/0.1/protein/<SHA-384 key of protein sequence>. The provenance of the feature pseudogene If this gene is a pseudo gene, indicate the type Feature added to the Gene feature, removed from all other features. Map the QTL is mapped on The type of recombination Reference Organism The actual reference of the citation Optionally define another reference sequence then the parent sequence object, this is for example needed for the mdg4 gene of Drosophila, which is transcript from two chromosomes. If the element to which the location belongs is defined on multiple sequence objects, this field is obligatory. A set of references associated to the GBOLDataSet regulatory_class The type of regulation Add to RegulationSite class, enumeration from the enumeration in genbank created The direction of the replication can be forward, reverse or both The reverse primer(s) The reverse primer(s) The reverse primer(s) rpt_type The type of the repeat RepeatType added, only present in the RepeatFeature class and subclasses rpt_unit_range Base range of the sequence that constitutes a repeated sequence Property of the repeat region SignalP properties Sample from which this piece of sequence originates from. All samples from which the sequence objects are collected satellite If repeat contains on or more satellites specify with this property the types of the satellites Satellite class added to describe the satellites, optional property of the repeat region The type of the satellite Sorted list of parts that upon concatenation forms the complete sequence. All dna objects included within the GBOL data set Identification of the material in a collection from which the sample is derived. Entries with more than one sampleSource indicates that the sequence was obtained from a sample that was deposited (by the submitter or a collaborator) in more than one collection. The regions that contain a spacer The strand on which it is positioned The type of the strand The type of secondary structure tag_peptide base location encoding the polypeptide for proteolysis tag of tmRNA and its termination codon; property of tmRNA, points to a Region The set of database that are target of the references associated to this link set An optional region to indicate to which part it is homologous to Taxon The rank of the taxon The type of taxon The taxonomy of the organism from which the sequence originates The lineage of the organism from which the sequence originates, should match to the lineage of the referenced taxonomy The topology of the sequence (linear, circular) All transcripts that are derived from the gene transl_except Indicate all codons, which have translation other then the default translation of the translation table TranslException object describes the translation exceptions on the CDS feature. Units used for the mapping e.g. Basepairs, centiMorgan The type of Variation Reference to the sequence of the virus, genes of the integrated virus can be annotated directly on genome as well as on the virus genome The agent which be performed this activity Reference to other entries holding entries with related information in other databases SignalP properties http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ Used to link an event such as a conference to an outcome (a product) of that event, for example, an article, a proceeding, etc. Used to link a bibliographic item to one of its contributor: can be an author, an editor, a publisher, etc. <dc:format> <dc:MediaTypeOrExtent> <rdf:value>text/html</rdf:value> <rdfs:label>HTML</rdfs:label> </dc:MediaTypeOrExtent> </dc:format> Used to describe the format of a bibliographic resource. Used to relate a reference citation to a bibliographic resource. Used to link a bibliographic item to its publisher. Parental rank Tells that this agent performed something for another agent. For example PFam domain scan actedOnBehalfOf InterproScan or a curator that actedOnBehalfOf the EBI. Description of each generated data set Description of each of the Data Sets used The agent that performed or initiated the activity that generated this entity Any entries used as input in the activity that created this entity The annotation activity that created this annotation result Denote the parent activity that initiated this task Cigar string describing alignment of alternate allele to reference Variant identification code PCR_conditions A textual description of the PCR conditions needed for this primer only present in primerBinding feature The abstract of the publication The time point at which the file was downloaded The accession id of the entry referenced Accepted same barcode ration The alignment length of two sequence objects allele List of names of known allele variants of the gene Alelle Count Frequency in which the alternate allele is found total number of alleles in called genotypes Read depth of alternate base Allele of the alternate sequence Any alternative names of the sequence altitude Altitude of the location from which the sample was collected in meters above or below nominal sea level Ancestral Allele The sequence of the anticodon use [TGAC] RNAmmer properties Barcode hits accepted Barcode hits accepted ratio RMS base quality Name of the binding moiety Biom file The bitscore of an alignment bound_moiety Textual description of the moiety recognizing the region Now linked to the biological recognized region should belong to biological recognized region, the bound_moiety being the identity that recognizes the reactions, which can be a sequence, protein, protein complex or any other molecule. SignalP properties Name of the membrane on the c terminal side cell_line The cell line from which the sequence was obtained, please use term from 'Cell Line Ontology' (http://www.clo-ontology.org/) where possible cell_type The cell type from which the sequence was obtained, please use term from 'Cell Ontology' (http://cellontology.org/) where possible Chimera ratio chromosome The chromosome name or number Both present on the sample and the chromosome object. Classify ratio clone If a clone library was used for sequencing, the sequence can originate from one or more clones clone_lib If a clone library was used for sequencing, specify the clone library Clustered read count The (GIT) repository containing the code of the tool codon_start If the start position is unknown, indicate with this property, where the first complete codon can be found Included in the exon as the reading frame can be shifted if the exon is part of a CDS The collection code of the collection within the given institute collection_date The date and time on which the specimen was collected. comment with additional information about the QTL Commit The String that uniquely identifies the last commit of the code used. The common name of the sequence compare The functional name Only present in Updated sequence feature, with a reference to the old sequence Textual description of the crosslink type cultivar The cultivar (cultivated variety) of plant from which sample was obtained. SignalP properties SignalP properties The version of the GBOL Data set, increase by 1 for every (set of) update(s) Date dbSNP membership Read depth quality An optional short description dev_stage The developmental stage at which the organism was when the sample was obtained ecotype The specific name of the host from which the sample has been collected, where the name indicates to which habitat/ecological environment the host has adopted to. Example: 'Columbia', which indicate that this Arabidopsis adopted itself with a hairier phenotype to deal with the especially sunny habitat. Effective length refers to the number of possible start sites a feature could have generated a fragment of that particular length E-mail environmental_sample This denotes that this sample is the result of a bulk NA extraction method, therefore the organism of the sample and associated sequence(s) are not (exactly) known. Error correction The estimated gap length, if not given its unknown and defaults to 100 Added to unknown assembly gap, to indicate the estimated length of the gap The probability of an alignment exception true Deprecated feature, which is imported from GenBank, mark a unconventional translation of the transcript deprecated, not be used any more in GBOL Expected allele counts(comma separated) The experimental evidence for the feature annotation (use Evidence Ontology term if possible) Forward barcode file name Forward barcode length Forward file name Forward primer length Forward read length FastQ set filter The date at which the record was first published The version of the record when it was first published Folder option Format Format URL Allele frequency frequency The frequency of this variation within the population Added to only natural variation feature, indicating the frequency of the variation function Short description of the function Added feature, every feature can have a textual function description, this is more broad then what genbank actually has Denote the length of the gap The nuber of gaps between two sequence objects Symbol of the gene (not the symbol of the resulting protein) Alternative/old gene symbols Generated by Genotype name of a sample for a specific variant Genotype quality Haplotype qualities haplogroup For the host from which the sample was obtained the name for a group of similar haplotypes that share some sequence variation. Haplogroups are often used to track migration of population groups. haplotype For the host from which the sample was obtained the name for a combination of alleles that are linked together on the same physical chromosome. In the absence of recombination, each haplotype is inherited as a unit, and may be used to track gene flow in populations. Type Number of Heterozygous variant samples The highlighted text of paper which is important The date until which the GBOL dataset should not published (only present on non public entries) The entity to which it is homologous to, being either another na sequence or cluster of na sequences An optional description of the element to which it is homologous to Number of Homozygous variant samples The Id used, typically typed as a prefix Identity level Identity 85 mismatch count Identity 90 mismatch count Identity 92 mismatch count Identity 95 mismatch count Identity 97 mismatch count The version of the sequence to include, should be specified if referenced resoure can have multiple versions. If not specified it referes to the first version. code of the institution taken from the list available at ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/coll_dump.txt isolate Individual isolate from which the sequence was obtained. For example ('Patient #152','DGGE band PSBAC-13') isolation_source Describes the physical, environmental and/or local geographical source of the biological sample from which the sequence was derived. Use geographicalLocation to denote the geographical location (examples: 'permanent Antarctic sea ice', 'rumen isolates from standard Pelleted ration-fed steer #67', 'denitrifying activated sludge from carbon limited continuous reactor') A list of keyword describing the content of the GBOL data set A description of a given object The last time the this GBOL data has been published The version of the version that has been last published latitude given in degrees. Positive is to the north, negative is to the south. Length of the sequence The letter of the COG group Level count Library number Genotype likelihoods comprised of comma separated floating point log10-scaled likelihoods for all possible genotypes given the set of alleles defined in the REF and ALT fields linkage group The local file name The local file path The locality (aka the name of a village) locus_tag Locus tag of the gene Added to gene class, any sub elements related to gene should have the same locus tag in the genbank file Log file longitude given in degrees. Positive is to the east, negative is to the west. macronuclear Indicates that this sequence from the macro-nuclear DNA from an organism which undergoes chromosomal differentiation between macro-nuclear and micro-nuclear stages. map The map location on the chromosome from which the sample was obtained (using PCR). Added to NAFeature, each DNA feature can a chromosome map location Unique map accession Identifier Map file The map location on the chromosome from which the sample was obtained. Name of the map the QTL were mapped on Mapping Quality Mark if more than one ASV identifier mating_type The mating type of the organism from which the sample was obtained. Mating type is used for prokaryotes, and for eukaryotes that undergo meiosis without sexually dimorphic gametes. For eukaryotic organisms that undergo meiosis with sexually dimorphic gametes please use the sex property. Matrix element type Matrix type Max chimera distance forward Max chimera distance reverse Max clustering mismatch count The maximum bit score obtained MD5sum of the file, not applicable to output files The COG membership class Additional sample metadata Minimum size of rejected OTU to be classify Minimum percentage threshold Mismatch count Mismatch DB Mismatch level count The number of mismatches between two sequence objects The name of the mobile element If applicable, the biological process in which this modification is involved. Use a Biological Process from the GO ontology. Short description denoted the state of the protein if the residue in the modified state. For example 'protein in active state' Name of the membrane on the n terminal side A name for the sample SignalP properties Number of hits Number of samples not called Number of samples with data old_locus_tag Old locus tag of the gene Added to gene class, any sub elements related to gene should have the same old locus tag in the genbank file Provenance applies to the given properties or the existence of the feature it self (use gbol:Existence), if not defined it all applies to all properties. Tag identifier of the operon The unique identifier to identify the scientist organelle Type of membrane-bound intracellular structure from which the sample was obtained. Use a 'cellular component' term from the GO ontology. The name of an organism P forward id P forward ratio P reverse id P reverse ratio p-value from Fisher's Exact Test The parameter string as used to start the software for the this activity, parameters referencing to another dataset used must be specified with {IRI}. So for example '-threshold 0.05 -i {:datasetIn1}'. Each of referenced input datasets must be also be referenced with the prov:used property The pattern used The percentage identity of a similarity analysis Phase quality Phase set phenotype Associated phenotypic property Added to feature, every feature can have an associated phenotypic effect phred scaled likelihood phred probabilities plasmid The name or identifier of plasmid from which the sample was obtained (using PCR). Present on the plasmid as 'plasmidName' and plasmid on the sample. The name of the plasmid pop_variant The name of the subpopulation or phenotype from which the sample was collected. The exact position (5 prime to 3 prime) Primer hits accepted Primer hits accepted ratio product Short description of the product resulting from the feature Product description only present in CDS Project protein_id The ID of the protein if translated from this CDS (format ^\\s*([A-Z]{3}\\d{5})(\\.)(\\d+)\\s*$) Added to the CDS, proteins can be merged from different species and therefore could have different identifiers when merged Note on the provenance proviral Indicates that this sequence is obtained from a virus or phage that is integrated into the genome of another organism Indicate that this sample is an proviral sequence extracted from another organism using PCR. Quality score of the marker Reverse barcode file name Reverse barcode length Reverse file name Reverse primer length Reverse read length Ratio Read count Read depth Number of reads in the file Actual Genotype of a sample for a specific variant rearranged Indicates if the sequence has undergone somatic rearrangement as part of an adaptive immune response. If equal to false it is the un-rearranged sequence that was inherited from the parental germ line. If equal to true the sequence has undergone somatic rearrangement as part of an adaptive immune response. If not defined it is not applicable to the sequence or unknown. The recommended name of the sequence Read depth of reference base Refernce database Allele of the reference sequence The region within the country or coast along the ocean relative position stop in centiMorgan relative position start in centiMorgan The release date of the database A free string to keep track of the release status (for private use, not present on public entries) The local file name The local file path replace Add to variation class, replace describes the new sequence. This needs further improvement * Old versus new or new versus old * make use of A>C standard format The residue type as defined within the 'Protein Modification Ontology' (http://www.psidev.info/MOD) Optional an URL it was downloaded from Optional a time point at which the file was downloaded ribosomal_slippage Indicate the presence of ribosomal slippage, the slippage region are excluded from the CDS using a CollectionOfRegions location for the CDS on the transcript. Boolean value indicating the presence of ribosomal slippage, slippage region are excluded from CDS using CollectionOfRegions location Rejected ASV Annotation rpt_family The family of the repeat Repeat family free string, no ontology yet connected rpt_unit_seq Pattern of the repeat. For example (NAG)8(WN)2 Property of the repeat feature, use string to note pattern SignalP properties SignalP properties The id of the sample within the given collection Specific name of the satellite The taxonomic name of the organism from which the sequence originates, should match to the name of the referenced taxonomy Score given by this method The optional secondary accession ids Secondary signature of the domain typically the interproscan ID segment The name or identifier of virus or phage (segment) from which the sample was obtained. The sequence, encoded with the default DNA or protein encoding The version of the sequence serotype The serological typing of the species within the sample by its antigenic properties sex The sex of the organism from which the sample was obtained. Sex is used for eukaryotic organisms that undergo meiosis with sexually dimorphic gametes. For prokaryotes, and for eukaryotes that undergo meiosis without sexually dimorphic gametes please use the mathingType property. The hash key of the sequence Shanon option The short name of the sequence SignalP properties If known specify target, use a 'cellular component' from the GO terms ontology The reference to signature of the domain (Gene3d, Pfam, etc) Optional short description of the signature Size of the file in bytes, not applicable to output files standard_name The standard name of the feature Added to gene feature, besides the gene property strain The name or identifier of the strain Strand bias sub_clone The name or identifier of the sub-clone from which the sample was obtained (using PCR). subcellular localization of a predicted protein sub_species The name or identifier of the sub-species from which the sample was obtained (using PCR). sub_strain The name or identifier of a genetically or otherwise modified strain from which the sample was obtained (using PCR). The parental strain from which it is derived should be annotated with the strain property. Symbol where the QTL was published under Taxon hit count The name of the taxon association term The textual description of the note Type tissue_lib The tissue library from which the sample was obtained tissue_type The tissue type from which the sample was obtained, use term from the 'BRENDA Tissue and Enzyme Source Ontology' whenever possible Total reads trait according to the Plant trait ontology: http://purl.obolibrary.org/obo/TO_0000661 trait name transl_table The translation table of the nucleotide sequence, if not present its inherited from the parent NASequence Added to the NAObject class, all features under this object use this translation table Turtle file Short description denoted the state of the protein if the residue in the unmodified state. For example 'protein in inactive state' Optional an URL it was downloaded from Used taxon level Validated Expression value variety The variety of the host from which the sample was derived. Use cultivar if the host is a cultivated plant. The version of the resource Number of wildtype samples SignalP properties Used to describe the creation date of a bibliographic item Use to link a bibliographic item to the date of an event. Check dc:created and other for proper specializations for this property A textual description of the dataset. The textual description of the version of the document, please not the version property in GBOLDataSet Used to describe the issue date of a bibliographic resource The language of this resource. Used to link a bibliographic resource to the language used to express it. A legal document giving official permission to do something with this dataset. It must be an IRI referencing to an resolvable URI returning the text of the license. Used to describe rights related to a bibliographic resource. Used to describe the subject of a bibliographic resource. The name of the dataset. http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ Used to name the locality of a publisher, an author, etc. http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ If available, the RDF dump of the dataset. An optional sparql endpoint to query the dataset A protocol endpoint for simple URI lookups for this data set. In cases where a simple string prefix match is insufficient, this property can be used. It expresses a regular expression pattern that matches the URIs of the dataset's entities. This property can be used to state that all entity URIs in a dataset start with a given string. In other words, they share a common “URI namespace”. Norms are not legally binding but represent the general principles or "code of conduct" adopted by a community for access and use of resources Best practice is use the URI of a waiver legal document as the value of this property. Used in describing structured values. Used to describe the content of a bibo:Document and other bibliographic resources. We suggest to use this property instead of the deprecated "bibo:content" one. A comment on the dataset Used to provide a human-readable version of a resource's name The time at which the activity is ended, if unknown set equal to startedAt. The time at which the activity is started The legal name of the organization Location to which the organization is based near Used to link an agent, related to bibliographic things, to a place where it is based near: can be a city, a monument, a building, etc. Image of the person use link to image Used to link an agent with an image that depict it. The familyName of the person, preferable use the surName property The first name of the person The given name of a person A homepage for some thing. Used to link an agent to its homepage (which is a web page accessible using a URL). Link to logo of organization mail address use URI scheme (see RFC 2368). A human readable (user) name of the agent The phone number of the entity The first name of the person Title of the person (Mr, Mrs, Ms, Dr. etc) empusa:EnumeratedValues 1 1 1 1 1 ASVSequence N/A 1 1 1 1 1 1 1 1 1 1 1 ASVSet #* The forward primer(s) forwardASV @:ASVSequence; #* The reverse primer(s) reverseASV @:ASVSequence?; #* Taxonomy assignedTaxon @:Taxon?; #* Taxon hit count taxonHitCount xsd:Integer?; #* Mismatch count mismatchCount xsd:Integer?; #* The type of taxon taxonType @:TaxonAssignmentType?; #* ASV identifier masterASVId xsd:string; #* Read count readCount xsd:Integer?; #* Ratio ratio xsd:Float?; #* Clustered read count clusteredReadCount xsd:Integer?; #* Used taxon level usedTaxonLevel xsd:Integer?; #* Mismatch level count mismatchLevelCount xsd:Integer*; #* ASV assignment asvAssignment @:ASVAssignment*; DocumentCore The definition of an ASV pair that can is a result of amplicon sequencing. 1 AminoAcid SequenceFeatureCore The set of all possible amino acids 1 1 AnnotationActivity #*- prov:startedAtTime xsd:dateTime; #*- prov:endedAtTime xsd:dateTime; true DocumentWiseProv 1 1 1 1 1 1 AnnotationSoftware #* The version of the resource version xsd:string; #* The (GIT) repository containing the code of the tool codeRepository IRI?; #* The String that uniquely identifies the last commit of the code used. commitId xsd:string?; #* A homepage for some thing. foaf:homepage xsd:string?; DocumentWiseProv 1 1 1 AntiCodon #* The position of the anticodon within the tRNA transcript antiCodingRegion @:Region; #* The encoded amino acid aminoAcid type::AminoAcid; #* The sequence of the anticodon use [TGAC] antiCodonSequence xsd:string; SequenceFeatureCore Complete description of an AntiCodon ArtificialRecognizedRegion SequenceFeatureCore A region on genomic sequence that is recognized by a men made entity or process. AssemblyAnnotation SequenceFeatureCore Annotation on the assembly of the sequence 1 1 1 1 AutomaticAnnotationActivity #* The parameter string as used to start the software for the this activity, parameters referencing to another dataset used must be specified with {IRI}. So for example '-threshold 0.05 -i {:datasetIn1}'. Each of referenced input datasets must be also be referenced with the prov:used property parameterString xsd:string; #* - wasAssociatedWith @:AnnotationSoftware?; DocumentWiseProv 1 Barcode N/A 1 1 BarcodeSet #* The forward primer(s) forwardBarcode @:Barcode?; #* The reverse primer(s) reverseBarcode @:Barcode?; DocumentCore The definition of a barcode pair that can be used for amplicon sequencing. Multiple forward and/or reverse barcodes might be defined. 1 1 BaseType SequenceFeatureCore The set of modified nucleic acids 1 1 BiologicalRecognizedRegion #*Textual description of the moiety recognizing the region boundMoiety xsd:string? SequenceFeatureCore A region on genomic sequence that is recognized by a biological entity or process. 1 1 1 1 Bowtie2 HD xsd:string; SQ xsd:string; PG xsd:string; CO xsd:string; 1 1 1 1 1 1 CDS #* Indicate the presence of ribosomal slippage, the slippage region are excluded from the CDS using a CollectionOfRegions location for the CDS on the transcript. ribosomalSlippage xsd:Boolean?; #* Indicate all codons, which have translation other then the default translation of the translation table translExcept @:TranslExcept*; #* Deprecated feature, which is imported from GenBank, mark a unconventional translation of the transcript exception xsd:string?; #* The resulting product protein when translating this CDS, each protein should have an IRI equal to http://gbol.life/0.1/protein/<SHA-384 key of protein sequence>. protein @:Protein; #* The ID of the protein if translated from this CDS (format ^\\s*([A-Z]{3}\\d{5})(\\.)(\\d+)\\s*$) proteinId xsd:string?; #* Short description of the product resulting from the feature product xsd:string?; #* If the start position is unknown, indicate with this property, where the first complete codon can be found codonStart xsd:PositiveInteger?; CDS SequenceFeatureCore Coding sequence; sequence of nucleotides that corresponds with the sequence of amino acids in a protein (location includes stop codon); feature includes amino acid conceptual translation. TransLExcept class added to ontology, only CDS has this property /codon_start has valid value of 1 or 2 or 3, indicating the offset at which the first complete codon of a coding feature can be found, relative to the first base of that feature; /transl_table defines the genetic code table used if other than the universal genetic code table; genetic code exceptions outside the range of the specified tables is reported in /transl_except qualifier; /protein_id consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point; when the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; 1 Chain SequenceFeatureCore A chain within the mature protein 1 Chromosome #* The chromosome name or number chromosome xsd:string?; SequenceFeatureCore A chromosomal sequence 1 1 Citation #* The actual reference of the citation reference @bibo:Document; #* The highlighted text of paper which is important highlight xsd:string?; DocumentCore A citation added to a feature 1 CollectionSampleType DocumentCore The types of collections in which a sample can be stored 1 1 CompleteNASequence #*- organism @:Organism; #* The type of the strand strandType type::StrandType; SequenceFeatureCore Complete sequences of physical nucleotide molecule. ConservedRegion SequenceFeatureCore Region within a protein that is conserved Contig #Optionally point to the reads, from which the contig is build. Use assembly property to define complete assembly. sourceReads @:Read*; SequenceFeatureCore An assembly of separate reads Country DocumentCore The list of all possible countries 1 1 1 1 1 Cufflinks confidenceHigh xsd:Double; confidenceLow xsd:Double; coverage xsd:Double; 1 DLoop D-loop SequenceFeatureCore Displacement loop; a region within mitochondrial DNA in which a short stretch of RNA is paired with one strand of DNA, displacing the original partner DNA strand in this region; also used to describe the displacement of a region of one strand of duplex DNA by a single stranded invader in the reaction catalyzed by RecA protein. DataFile #* Optional list of entities that are contained within the file containedEntity @prov:Entity*; DocumentWiseProv An independent file on local disk or remote repository. 1 1 1 Database #* The Id used, typically typed as a prefix id xsd:string ; #* The version of the resource version xsd:string?; #* The release date of the database releaseDate xsd:DateTime?; DocumentWiseProv The description of the database containing entities to which XREF elements can reference to. EntryType DocumentCore The GBOL document entry types, based on the genbank division types. 1 Exon exon SequenceFeatureCore region of genome that codes for portion of spliced mRNA,rRNA and tRNA; may contain 5'UTR, all CDSs and 3' UTR; 1 1 1 ExonList #The exons within the list exon @:Exon+=; #* The provenance of the feature provenance @:Provenance?; #* Associated phenotypic property phenotype xsd:string?; DocumentCore 1 1 Experiment #* Read data used as input inputReads @:ReadInformation; #* The provenance of the feature provenance @:Provenance; Insilico experiment performed such as RNAseq mapping 1 1 1 1 ExpressionType 1 1 1 1 1 1 Feature :location :provenance #Location objects location @:Location; #* Any publication associated to feature annotation citation @:Citation*; #* The standard name of the feature standardName xsd:string?; #* Short description of the function function xsd:string?; #* The provenance of the feature provenance @:FeatureProvenance+; #* Reference to other entries holding entries with related information in other databases xref @:XRef*; #* A set off some additional notes note @:Note*; #* Indicate that the location is artificial because of a heterogeneous population for low quality sequence region artificialLocation type::ReasonArtificialLocation?; #* Associated phenotypic property phenotype xsd:string?; #* The accession id of the entry referenced accession xsd:string*; true SequenceFeatureCore Adds a functional description to a range or multiple ranges of a biological sequence. FileType FivePrimeUTR 5'UTR SequenceFeatureCore region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein; 1 1 1 GapType SequenceFeatureCore Belongs to the gapType property, full definition of the AGP Specification need to be made. 1 1 1 1 1 GenomicFeature #* Operon to which the genetic element belongs to operon @:Operon?; true SequenceFeatureCore All features that can be present on a genome 1 1 GeographicalCoordinate #* longitude given in degrees. Positive is to the east, negative is to the west. longitude xsd:Double; #* latitude given in degrees. Positive is to the north, negative is to the south. latitude xsd:Double; DocumentCore Location denotes by its geographical coordinates 1 1 GeographicalLocation #* The region within the country or coast along the ocean region xsd:string?; #* The locality (aka the name of a village) locality xsd:string?; true DocumentCore 1 Homology #* The entity to which it is homologous to, being either another na sequence or cluster of na sequences homologousTo IRI; SequenceFeatureCore Denote a region to be homologous to another entity, which is either another na sequence or cluster of na sequences 1 ImmunoglobulinFeature #* The type of the immunoglobulin region immunoglobulinRegionType type::ImmunoglobulinRegionType; SequenceFeatureCore ImmunoglobulinRegionType 1 1 1 1 1 1 IntegratedVirus #* Reference to the sequence of the virus, genes of the integrated virus can be annotated directly on genome as well as on the virus genome virusGenome @:NASequence?; #* The region of the virus genome that is integrated integratedRegion @:Location; SequenceFeatureCore A virus genome integrated into another genome 1 Interleaved #Insert size if paired-end insertSize xsd:Integer?; 1 1 IntraMembraneRegion #* Name of the membrane on the n terminal side nTerminalMembrane xsd:string?; #* Name of the membrane on the c terminal side cTerminalMembrane xsd:string?; SequenceFeatureCore Region in-between two membranes Intron iDNA intron SequenceFeatureCore a segment of DNA that is transcribed, but removed from within the transcript by splicing together the sequences(exons) on either side of it; 1 Kallisto #* Effective length refers to the number of possible start sites a feature could have generated a fragment of that particular length eff_length xsd:Double; 1 LandBasedGeographicalLocation #* The country country type::Country; DocumentCore A geographical location on land, identified by a country name 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Library #* Library number libraryNum xsd:Integer; #* Forward file name fFile xsd:string; #* Reverse file name rFile xsd:string; #* Forward barcode file name fBarcodeFile xsd:string?; #* Reverse barcode file name rBarcodeFile xsd:string?; #* Total reads totalReads xsd:Integer; #* Primer hits accepted primerHitsAccepted xsd:Integer; #* Primer hits accepted ratio primerHitsAcceptedRatio xsd:float; #* Barcode hits accepted barcodeHitsAccepted xsd:Integer; #* Barcode hits accepted ratio barcodeHitsAcceptedRatio xsd:float; #* Accepted same barcode ration accpetedSameBarcodeRatio xsd:float; #* Forward barcode length fBarcodeLength xsd:Integer; #* Reverse barcode length rBarcodeLength xsd:Integer; #* Sample from which this piece of sequence originates from. sample @:Sample+; #* The provenance of the feature provenance @:Provenance; LinkageEvidence SequenceFeatureCore All types of evidence possible to link to contigs together into one scaffold 1 1 1 1 1 1 1 1 LocalDataFile #* The local file name localFileName xsd:string; #* The local file path localFilePath xsd:string; #* Optional an URL it was downloaded from retrievedFrom IRI?; #* Optional a time point at which the file was downloaded retrievedOn xsd:DateTime?; #* Optionally set the fileType fileType type::FileType?; #* MD5sum of the file, not applicable to output files md5 xsd:string?; #* Size of the file in bytes, not applicable to output files size xsd:Long?; DocumentWiseProv A file on the local disk 1 1 1 1 1 1 1 LocalSequenceFile StrandOrientation type::ReadOrientation?; sequencer type::SequencingPlatform?; adapter xsd:string?; sequencingDepth xsd:Integer?; #* Number of reads in the file reads xsd:Long; #Length of reads in the file readLength xsd:Long; #Total number of bases in the file bases xsd:Long; A sequence file on the local disk of the type FASTA or FASTQ 1 1 MapUnits Defines the units used to map the QTLs to the genome 1 1 1 1 MaterialSource #* code of the institution taken from the list available at ftp://ftp.ncbi.nlm.nih.gov/pub/taxonomy/coll_dump.txt institutionCode xsd:string; #* The collection code of the collection within the given institute collectionCode xsd:string; #* The id of the sample within the given collection sampleId xsd:string?; #* Type of the collection sample collectionSampleType type::CollectionSampleType DocumentCore Describes a sample within a (long term storage) collection. MaturedRNA SequenceFeatureCore A sequence of a matured transcript 1 MiscNA SequenceFeatureCore Anything that is not a miscellaneous transcript, not a chromosome, not a plasmid or uncomplete NA sequence 1 MiscRecomb #* The type of recombination recombinationType type::RecombinationType misc_recomb SequenceFeatureCore Site of any generalized, site-specific or replicativere combination event where there is a breakage and reunion of duplex DNA that cannot be described by other recombination keys or qualifiers of source key(/proviral); 1 MiscRna #* Short description of the product resulting from the feature product xsd:string?; misc_RNA SequenceFeatureCore Any transcript that cannot be defined by other transcript types (precursor_RNA, mRNA, ncRNA, rRNA, tmRNA and tRNA); MiscStructure misc_structure SequenceFeatureCore any secondary or tertiary nucleotide structure or conformation that cannot be described by other Structure keys (stem_loop and D-loop); 1 1 MobileElement #* Mobile element type mobileElementType type::MobileElementType; #* The name of the mobile element mobileElementName xsd:string; mobile_element SequenceFeatureCore Region of genome containing mobile elements; MobileElementType SequenceFeatureCore All types of mobile elements 1 1 1 1 1 1 ModifiedResidue #* The residue type as defined within the 'Protein Modification Ontology' (http://www.psidev.info/MOD) residue IRI; #* If applicable, the biological process in which this modification is involved. Use a Biological Process from the GO ontology. modificationFunction IRI?; #* Short description denoted the state of the protein if the residue in the modified state. For example 'protein in active state' modifiedState xsd:string?; #* Short description denoted the state of the protein if the residue in the unmodified state. For example 'protein in inactive state' unmodifiedState xsd:string?; SequenceFeatureCore Denotes a modified residue or residue that is typically modified within a protein 1 MoietyBindingSite #* Name of the binding moiety bindingMoiety xsd:string; SequenceFeatureCore Region of the protein that bind to some moiety NABindingSite SequenceFeatureCore #* If known specify the Protein binding region on the dna or rna bindingRegion ProteinBinding?; #* If unknown give a short description of the region to which this side within the protein binds to. bindingRegionDesc xsd:string?; Region that bind to a dna or rna molecule. 1 NAFeature #* The map location on the chromosome from which the sample was obtained. mapLocation xsd:string?; #* Expression feature expression @:Expression*; true SequenceFeatureCore 1 1 1 1 1 1 1 1 NomenclaturalType DocumentCore List of nomenclature types used to annotate a taxonomic entry. 1 1 Ocean DocumentCore 1 OneOfPosition #A list of exact positions on which the position could be located (5 prime to 3 prime) position xsd:long+; LocationCore A position that can be either at one of the given positions. We currently have no support to include InRange, Before or After positions. If needed please notify us. Taken over from Faldo ontology, although Faldo ontology does allow for inclusion of regions. This causes the possibility of an ill defined loop as region can include OneOfPosition again, which has no semantical meaning. 1 Operon #*Tag identifier of the operon operonId xsd:string?; operon SequenceFeatureCore Region containing polycistronic transcript including a cluster of genes that are under the control of the same regulatory sequences/promotor and in the same biological pathway 1 1 Organism #* The taxonomy of the organism from which the sequence originates taxonomy @:TaxonomyRef?; #* The taxonomic name of the organism from which the sequence originates, should match to the name of the referenced taxonomy scientificName xsd:string?; #* The lineage of the organism from which the sequence originates, should match to the lineage of the referenced taxonomy taxonomyLineage @:Taxon*; DocumentCore The living envelope in which all SequenceObject are enclosed. PCRPrimer DocumentCore A single primer. 1 1 PCRPrimerSet #* The forward primer(s) forwardPrimer @:PCRPrimer; #* The reverse primer(s) reversePrimer @:PCRPrimer?; DocumentCore The definition of a primer pair that can be used for a PCR. Multiple forward and/or reverse primers might be defined. 1 1 PairedEnd file2 @:LocalSequenceFile; #Insert size if paired-end insertSize xsd:Integer?; 1 PartGapKnownLength #* Denote the length of the gap gapLength xsd:PositiveInteger SequenceFeatureCore A gap within the assembly with a known length 1 PartIncludedSequence #* Reference to the sequence that is included includedSequence @:UncompleteNASequence; SequenceFeatureCore A part of the sequence included from another sequence that is included within the same GBOL document. 1 PartSequence #* The included region of referenced sequence, only exact position must be used to denote the start en end region, reference property should be empty. Use the strand property to include forward or reverse complement strand. includedRegion @:Region; true SequenceFeatureCore A part of the sequence included from another sequence. 1 1 PartXRefSequence #* The xref from which the sequence is included includedXRefSequence @:XRef; #* The version of the sequence to include, should be specified if referenced resoure can have multiple versions. If not specified it referes to the first version. includedXRefVersion xsd:string?; SequenceFeatureCore A part of the sequence included from another sequence that is included from an externally referenced resource. 1 Plasmid #*The name of the plasmid plasmidName xsd:string?; SequenceFeatureCore A plasmid sequence PolyASite polyA_site SequenceFeatureCore Site on an RNA transcript to which will be added adenine residues by post-transcriptional polyadenylation; 1 ProPeptide SequenceFeatureCore The part of a protein that is proteolytically cleaved during the protein's maturation, e.g. the internal residues of proinsulin, the N-terminal residues of pepsinogen. If the propeptide is a signal peptide please use the SingalPeptide class. 1 1 1 ProteinDomain #* The reference to signature of the domain (Gene3d, Pfam, etc) signature IRI; #* Secondary signature of the domain typically the interproscan ID secondarySignature IRI*; #* Optional short description of the signature signatureDesc xsd:string?; #* Option to denote the type of domain domainType type::ProteinDomainType?; SequenceFeatureCore A conserved domain or family within a protein ProteinDomainType SequenceFeatureCore A list of types for a pattern such as a hidden markov model. ProteinFeature SequenceFeatureCore Some of the subclasses are based on the ontology found in the metacyc database http://bioinformatics.ai.sri.com/ptools/protein-features-ontology.html 1 1 1 ProteinHomology #* The entity to which it is homologous to, being either another na sequence or cluster of na sequences homologousTo IRI; #* An optional description of the element to which it is homologous to homologousToDesc xsd:string?; #* An optional region to indicate to which part it is homologous to targetRegion @:Region? SequenceFeatureCore Denote a region to be homologous to another entity, which is either another protein or cluster of proteins 1 ProteinInteractionSite #* If known, a region within another protein that binds this region. If region of other protein is unknown use fuzzy position from begin to end. bindingProtein @:ProteinInteractionSite?; SequenceFeatureCore Region of the protein that bind to another protein 1 1 ProteinRepeat #* Base range of the sequence that constitutes a repeated sequence rptUnitRange @:Region?; #* Pattern of the repeat. For example (NAG)8(WN)2 rptUnitSeq xsd:string?; SequenceFeatureCore A repeat within a protein 1 ProteinStructure #* The type of secondary structure structureType type::ProteinStructureType; SequenceFeatureCore Defines the secondary structure of the protein for the given region ProteinStructureType SequenceFeatureCore The secondary protein structure types. 1 1 1 1 1 ProvenanceAnnotation #* Note on the provenance provenanceNote xsd:string?; #* The actual reference of the citation reference @bibo:Document; #* The experimental evidence for the feature annotation (use Evidence Ontology term if possible) experimentalEvidence xsd:string?; #* Optionally give a list of features upon which it is based derivedFrom @:Feature*; ElementWiseProv The element wise annotation of the provenance. This element is typically related to one feature or qualifier, but can be shared among multiple. ProvenanceApplication ProvenanceAssembly ElementWiseProv ProvenanceClassification PseudoGeneType SequenceFeatureCore A list of reasons for gene to be a pseudo gene. 1 1 PublicDataFile #* Optional an URL it was downloaded from url IRI?; #* The time point at which the file was downloaded accessedOn xsd:DateTime?; DocumentWiseProv A public file that is available on the INTERNET 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 QTL #* associated markers linked to the QTL region associatedFeature @:Feature*; #* Map the QTL is mapped on qtlMap @:QTLMap?; #* Parental strains parent @:Organism*; #* trait according to the Plant trait ontology: http://purl.obolibrary.org/obo/TO_0000661 trait IRI*; #* trait name traitName xsd:string?; #* The accession id of the entry referenced accession xsd:string?; #* The type of QTL Type type::QTLTypes; #* Symbol where the QTL was published under symbol xsd:string?; #* comment with additional information about the QTL comment xsd:string?; #* linkage group linkageGroup xsd:string?; #* association term term xsd:string*; #* relative position start in centiMorgan relativeStart xsd:double?; #* relative position stop in centiMorgan relativeEnd xsd:double?; SequenceFeatureCore Quantitative Trait Loci 1 1 1 QTLTypes The type of a QTL, this is the method used to map the QTL 1 Read SequenceFeatureCore A single read from a sequencer. 1 1 1 1 1 1 ReadInformation #Length of reads readLength xsd:Long?; #Total number of bases bases xsd:long?; file @:LocalSequenceFile+; #Machine used for sequencing... machine xsd:string?; center xsd:string?; adapter xsd:string?; ReadOrientation ReasonArtificialLocation SequenceFeatureCore Reasons why a given location is based on an artificial location. RecognizedRegion SequenceFeatureCore A region on genomic sequence that is recognized by another entity or process. RecombinationType SequenceFeatureCore 1 1 1 1 RegulatoryClass SequenceFeatureCore A list type for regulatory elements. RejectedASV 1 1 1 1 RejectedAsChimera #* P forward id pForwardId xsd:Integer; #* P forward ratio pForwardRatio xsd:float; #* P reverse id pReverseId xsd:Integer; #* P reverse ratio pReverseRatio xsd:float; 1 1 1 1 1 1 1 RemoteDataFile #* The local file name remoteFileName xsd:string; #* The local file path remoteFilePath xsd:string; #* Optional an URL it was downloaded from retrievedFrom IRI?; #* Optional a time point at which the file was downloaded retrievedOn xsd:DateTime?; #* Optionally set the fileType fileType type::FileType?; #* MD5sum of the file, not applicable to output files md5 xsd:string?; #* Size of the file in bytes, not applicable to output files size xsd:Long?; DocumentWiseProv A file on a remote disk 1 1 1 1 1 1 1 RemoteSequenceFile StrandOrientation type::ReadOrientation?; sequencer type::SequencingPlatform?; adapter xsd:string?; sequencingDepth xsd:Integer?; #* Number of reads in the file reads xsd:Long; #Length of reads in the file readLength xsd:Long; #Total number of bases in the file bases xsd:Long; A sequence file on a remote disk of the type FASTA or FASTQ 1 1 1 1 RepeatFeature #* The family of the repeat rptFamily xsd:string?; #* The type of the repeat rptType type::RepeatType?; #* Base range of the sequence that constitutes a repeated sequence rptUnitRange @:Region?; #* Pattern of the repeat. For example (NAG)8(WN)2 rptUnitSeq xsd:string?; #* If repeat contains on or more satellites specify with this property the types of the satellites satellite @:Satellite*; SequenceFeatureCore Feature for which a repetitive unit can be defined RepeatRegion repeat_region SequenceFeatureCore Region of genome containing repeating units; RepeatType SequenceFeatureCore A list of repeat types within a genome. 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Sample #* A name for the sample name xsd:string; #* An optional short description description xsd:string?; #* Any publication associated to feature annotation citation @:Citation*; #* Reference to other entries holding entries with related information in other databases xref @:XRef*; #* A set off some additional notes note @:Note*; #* Identification of the material in a collection from which the sample is derived. Entries with more than one sampleSource indicates that the sequence was obtained from a sample that was deposited (by the submitter or a collaborator) in more than one collection. sourceMaterial @:MaterialSource*; #The primers used to get to get the sample from the collected material. The sample is the PCR product if the property is defined. PCRPrimers @:PCRPrimerSet?; #* Barcode sequence set barcodes @:BarcodeSet?; #* ASV sequence set asv @:ASVSet*; #* Describes the physical, environmental and/or local geographical source of the biological sample from which the sequence was derived. Use geographicalLocation to denote the geographical location (examples: 'permanent Antarctic sea ice', 'rumen isolates from standard Pelleted ration-fed steer #67', 'denitrifying activated sludge from carbon limited continuous reactor') isolationSource xsd:string?; #* This denotes that this sample is the result of a bulk NA extraction method, therefore the organism of the sample and associated sequence(s) are not (exactly) known. environmentalSample xsd:boolean?; #* Altitude of the location from which the sample was collected in meters above or below nominal sea level altitude xsd:Double?; #* The persons or institute who collected the specimen collectedBy @foaf:Agent*; #* The date and time on which the specimen was collected. collectionDate xsd:dateTime?; #* The geographical location(country or ocean) from which the sample is collected geographicalLocation @:GeographicalLocation?; #* The geographical coordinates(latitude + longitude) of the location where the specimen was collected geographicalCoordinate @:GeographicalCoordinate?; #* The developmental stage at which the organism was when the sample was obtained devStage xsd:string?; #* The name of the expert who identified the specimen taxonomically identifiedBy @foaf:Agent?; #* Individual isolate from which the sequence was obtained. For example ('Patient #152','DGGE band PSBAC-13') isolate xsd:string?; #* The tissue library from which the sample was obtained tissueLib xsd:string?; #* The tissue type from which the sample was obtained, use term from the 'BRENDA Tissue and Enzyme Source Ontology' whenever possible tissueType xsd:string?; #* Type of membrane-bound intracellular structure from which the sample was obtained. Use a 'cellular component' term from the GO ontology. organelle IRI?; #* The serological typing of the species within the sample by its antigenic properties serotype xsd:string?; #* The specific name of the host from which the sample has been collected, where the name indicates to which habitat/ecological environment the host has adopted to. Example: 'Columbia', which indicate that this Arabidopsis adopted itself with a hairier phenotype to deal with the especially sunny habitat. ecotype xsd:string?; #* For the host from which the sample was obtained the name for a group of similar haplotypes that share some sequence variation. Haplogroups are often used to track migration of population groups. haplogroup xsd:string?; #* For the host from which the sample was obtained the name for a combination of alleles that are linked together on the same physical chromosome. In the absence of recombination, each haplotype is inherited as a unit, and may be used to track gene flow in populations. haplotype xsd:string?; #* The cultivar (cultivated variety) of plant from which sample was obtained. cultivar xsd:string?; #* The cell line from which the sequence was obtained, please use term from 'Cell Line Ontology' (http://www.clo-ontology.org/) where possible cellLine xsd:string?; #* The cell type from which the sequence was obtained, please use term from 'Cell Ontology' (http://cellontology.org/) where possible cellType xsd:string?; #* The host of the organism (from which the sample was obtained), which it lives in, upon or attached to in its natural environment. host @:TaxonomyRef?; #* Scientific name of the laboratory host used to propagate the source organism from which the sample was obtained. The full binomial scientific name of the host organism should be used when known. Extra conditional information relating to the host may also be included. For example '12 year old human with IBD' for a gut bacteria. labHost xsd:string?; #* The mating type of the organism from which the sample was obtained. Mating type is used for prokaryotes, and for eukaryotes that undergo meiosis without sexually dimorphic gametes. For eukaryotic organisms that undergo meiosis with sexually dimorphic gametes please use the sex property. matingType xsd:string?; #* The sex of the organism from which the sample was obtained. Sex is used for eukaryotic organisms that undergo meiosis with sexually dimorphic gametes. For prokaryotes, and for eukaryotes that undergo meiosis without sexually dimorphic gametes please use the mathingType property. sex xsd:string?; #* The name of the subpopulation or phenotype from which the sample was collected. popVariant xsd:string?; #* The variety of the host from which the sample was derived. Use cultivar if the host is a cultivated plant. variety xsd:string?; #* The name or identifier of virus or phage (segment) from which the sample was obtained. segment xsd:string?; #* The chromosome name or number chromosome xsd:string?; #* The map location on the chromosome from which the sample was obtained (using PCR). map xsd:string?; #* The name or identifier of plasmid from which the sample was obtained (using PCR). plasmid xsd:string?; #*The name or identifier of the strain strain xsd:string?; #* The name or identifier of the sub-clone from which the sample was obtained (using PCR). subClone xsd:string?; #* The name or identifier of the sub-species from which the sample was obtained (using PCR). subSpecies xsd:string?; #* The name or identifier of a genetically or otherwise modified strain from which the sample was obtained (using PCR). The parental strain from which it is derived should be annotated with the strain property. subStrain xsd:string?; #* Indicate that this sample is an proviral sequence extracted from another organism using PCR. proviralExtraction xsd:boolean?; #* Additional sample metadata metadata IRI*; DocumentCore Description of the biological sample. Each sequence should define from which sample they are derived. # removed & moved #bioMaterial xsd:string?; #cultureCollection xsd:string?; #specimenVoucher xsd:string?; #--> merged to sourceMaterial, use collectionSampleType to identify type #country type::Country?; -> replaced with geographicalLocation #latLon-> replaced with geographicalCoordinate #serovar xsd:string?; -> killed store under seroType #focus xsd:boolean?; --> replaced with the integratedInto property in the sequence object #transgenic xsd:boolean?; --> replaced with the integratedInto property in the sequence object #mol_type --> removed replaced with strandType & NASequence subclasses #germline xsd:boolean?; --> moved to sequence & removed replace with rearranged = false #rearranged xsd:boolean?; --> moved to sequence #clone xsd:string?; --> move to sequence, is a bit outdated now a days #cloneLib xsd:string?; --> move to sequence, is a bit outdated now a days #proviral xsd:boolean?; --> moved to sequence & set proviralExtraction = true on sample #division --> removed information already captures by the taxonomy property #organism --> replaced with taxonomy in organism object linked to sequence object #type_material --> replaced with the nomenclaturalType in the TaxonomyRef under the Sequence object 1 1 Satellite #* The type of the satellite satelliteType type::SatelliteType; #* Specific name of the satellite satelliteName xsd:string; DocumentCore A DNA satellite SatelliteType SequenceFeatureCore A list of satellite types Scaffold #Optionally point to the contigs, from which the Scaffold is build. Use assembly property to define complete assembly. sourceContigs @:Contig*; SequenceFeatureCore A scaffolded set of contigs. 1 1 1 1 1 1 1 1 1 1 1 1 1 SequenceAnnotation SequenceFeatureCore Annotation on the sequence itself 1 1 SequencePart true SequenceFeatureCore A part within a sequence assembly. SequenceSet SequencingPlatform 1 SignalPeptide #* If known specify target, use a 'cellular component' from the GO terms ontology signalTarget IRI? sig_peptide SequenceFeatureCore The sequence holding the targeting information used to post-translationally export or import a sequence into any of the organels. This amino acid terminal sequence is typically removed during or shortly after import or export. SingleEnd 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 Star startedMappingOn xsd:string; finishedMappingOn xsd:string; mappingSpeedMillionOfReadsPerHour xsd:Float; numberOfInputReads xsd:Integer; averageInputReadLength xsd:Float; uniquelyMappedReadsNumber xsd:Integer; uniquelyMappedReadsPercentage xsd:Float; averageMappedLength xsd:Float; numberOfSplicesTotal xsd:Integer; numberOfSplicesAnnotated_sjdb xsd:Integer; numberOfSplicesGT_AG xsd:Integer; numberOfSplicesGC_AG xsd:Integer; numberOfSplicesAT_AC xsd:Integer; numberOfSplicesNonCanonical xsd:Integer; mismatchRatePerBasePercentage xsd:Float; deletionRatePerBase xsd:Float; deletionAverageLength xsd:Float; insertionRatePerBase xsd:Float; insertionAverageLength xsd:Float; numberOfReadsMappedToMultipleLoci xsd:Integer; percentageOfReadsMappedToMultipleLoci xsd:Float; numberOfReadsMappedToTooManyLoci xsd:Integer; percentageOfReadsMappedToTooManyLoci xsd:Float; percentageOfReadsUnmappedTooManyMismatches xsd:Float; percentageOfReadsUnmappedTooShort xsd:Float; percentageOfReadsUnmappedOther xsd:Float; numberOfChimericReads xsd:Integer; percentageOfChimericReads xsd:Float; StemLoop stem_loop SequenceFeatureCore hairpin; a double-helical region formed by base-pairing between adjacent (inverted) complementary sequences in a single strand of RNA or DNA. StrandType SequenceFeatureCore The list of types for a nucleic acid strand StructureFeature SequenceFeatureCore 1 1 1 Taxon #* The name of the taxon taxonName xsd:string; #* The rank of the taxon taxonRank type::Rank; #* Parental rank rdfs:subClassOf @:Taxon?; DocumentCore Simple taxon class to define a taxon in a lineage TaxonAssignmentType 1 TaxonomyRef # The context (a nomenclatural type) in which the taxonomy is referenced nomenclaturalType type::NomenclaturalType?; DocumentCore A xref which point to a database containing taxomic classification, which is typically the uniprot taxonomic database. 1 ThreePrimeUTR 3'UTR SequenceFeatureCore Region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein TopHat Topology DocumentCore The topology of a nucleic acid string TransMembraneRegion SequenceFeatureCore Region of the protein that is within a membrane 1 Transcript #* This list off exons that form this transcript, in case of prokaryote it contains one element exonList @:ExonList?; #* The set of features annotating the sequence feature @:TranscriptFeature*; SequenceFeatureCore Sequence of nucleotide molecule created after transcription No provenance included here, as sequence object represent a sequence that might originate either from a sample or an exonlist. The exon list caries the provenance, as this the element that is/can be predicted. TranscriptFeature SequenceFeatureCore Features on a transcript TranscriptionElement true SequenceFeatureCore Elements related to transcribed regions 1 1 TranslExcept #* The position of region which translate to other amino acid then the default translation table exceptRegion @:Region; #* The encoded amino acid aminoAcid type::AminoAcid; SequenceFeatureCore 1 UncompleteNASequence #* The type of the strand strandType type::StrandType; SequenceFeatureCore Incomplete sequence of a physical nucleotide molecule 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 VariantGenotype #* Genotype name of a sample for a specific variant genotypeName xsd:string?; #* Genotypes of the sample the variant was called on genotype @:VariantGenotype*; #* Actual Genotype of a sample for a specific variant realGenotype xsd:string?; #* Genotype quality genotypeQuality xsd:string?; #* Read depth readDepth xsd:string?; #* Read depth quality depthQuality xsd:string?; #* Read depth of reference base refDepth xsd:string?; #* Read depth of alternate base altDepth xsd:string?; #* p-value from Fisher's Exact Test pVal xsd:string?; #* Allele frequency freq xsd:string?; #* filter filter xsd:string?; #* Genotype likelihoods comprised of comma separated floating point log10-scaled likelihoods for all possible genotypes given the set of alleles defined in the REF and ALT fields likelihood xsd:string?; #*phred scaled likelihood phredLikelihood xsd:Integer?; #*phred probabilities phredProb xsd:Float?; #*Haplotype qualities haploQuality xsd:string?; #*Phase set phaseSet xsd:string?; #* Phase quality phaseQuality xsd:Integer?; #*Expected allele counts(comma separated) expectedAlleleCounts xsd:string?; #*Mapping Quality mapQuality xsd:String?; #*The name or identifier of the strain strain xsd:string?; #* Reference Organism refOrganism @:Organism?; #* Alternative Organism altOrganism @:Organism?; Defines a genotype for a called Variation in the Variation class 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 VariationFeature #The sequence replacing the original sequence replace xsd:string?; true SequenceFeatureCore Annotation on the sequence of modified bases in comparison to VariationTypes Type of the variation entry 1 WaterBasedGeographicalLocation #* The name of the ocean ocean type::Ocean; DocumentCore A geographical location in a ocean, identified by an ocean name 1 1 1 XRef #*The database to with the links link to db @:Database; #* The accession id of the entry referenced accession xsd:string; #* The optional secondary accession ids secondaryAccession xsd:string*; #* The provenance of the feature provenance @:XRefProvenance; DocumentCore 1 mRNA mRNA SequenceFeatureCore messenger RNA; includes 5'untranslated region (5'UTR),coding sequences (CDS, exon) and 3'untranslated region(3'UTR); 1 1 ncRNAType SequenceFeatureCore http://www.insdc.org/rna_vocab.html List of non coding RNA types. 1 1 1 tRNA #* The anti codon of the TRNA anticodon @:AntiCodon?; #* Short description of the product resulting from the feature product xsd:string?; tRNA SequenceFeatureCore mature transfer RNA, a small RNA molecule (75-85 bases long) that mediates the translation of a nucleic acid sequence into an amino acid sequence 1 1 tmRNA #* base location encoding the polypeptide for proteolysis tag of tmRNA and its termination codon; tagPeptide @:Region?; #* Short description of the product resulting from the feature product xsd:string?; tmRNA SequenceFeatureCore transfer messenger RNA; tmRNA acts as a tRNA first,and then as an mRNA that encodes a peptide tag; the ribosome translates this mRNA region of tmRNA and attaches the encoded peptide tag to the C-terminus of the unfinished protein; this attached tag targets the protein for destruction or proteolysis; 1 1 dc:MediaTypeOrExtent #* Used in describing structured values. rdf:value xsd:string?; #* Used to provide a human-readable version of a resource's name rdfs:label xsd:string; BIBO 1 1 1 1 1 1 1 bibo:Event bibo:presents @bibo:Document*; bibo:organizer @foaf:Agent*; bibo:place xsd:string*; BIBO An arbitrary classification of a space/time region, by a cognitive agent. An event may have actively participating agents, passive factors, products, and a location in space/time. 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 void:Dataset #* The name of the dataset. dc:title xsd:string? ; #* A textual description of the dataset. dc:description xsd:string?; #* A comment on the dataset rdfs:comment xsd:string?; #* Used to provide a human-readable version of a resource's name rdfs:label xsd:string?; #* A legal document giving official permission to do something with this dataset. It must be an IRI referencing to an resolvable URI returning the text of the license. dc:license IRI?; #* The textual description of the version of the document, please not the version property in GBOLDataSet dc:hasVersion xsd:string; #* Norms are not legally binding but represent the general principles or "code of conduct" adopted by a community for access and use of resources wv:norms IRI?; #* Best practice is use the URI of a waiver legal document as the value of this property. wv:waiver xsd:string?; #* An optional sparql endpoint to query the dataset void:sparqlEndpoint IRI?; #* If available, the RDF dump of the dataset. void:dataDump IRI?; #* This property can be used to state that all entity URIs in a dataset start with a given string. In other words, they share a common “URI namespace”. void:uriSpace IRI?; #* In cases where a simple string prefix match is insufficient, this property can be used. It expresses a regular expression pattern that matches the URIs of the dataset's entities. void:uriRegexPattern xsd:string?; #* A protocol endpoint for simple URI lookups for this data set. void:uriLookupEndpoint IRI?; #* The language of this resource. dc:language xsd:string*; DocumentCore The fundamental concept of VoID is the dataset. A dataset is a set of RDF triples that are published, maintained or aggregated by a single provider. Unlike RDF graphs, which are purely mathematical constructs [RDF-CONCEPTS], the term dataset has a social dimension: we think of a dataset as a meaningful collection of triples, that deal with a certain topic, originate from a certain source or process, are hosted on a certain server, or are aggregated by a certain custodian. Also, typically a dataset is accessible on the Web, for example through resolvable HTTP URIs or through a SPARQL endpoint, and it contains sufficiently many triples that there is benefit in providing a concise summary. Since most datasets describe a well-defined set of entities, datasets can also be seen as a set of descriptions of certain entities, which often share a common URI prefix (such as http://dbpedia.org/resource/). In VoID, a dataset is modeled as an instance of the void:Dataset class. Such a void:Dataset instance is a single RDF resource that represents the entire dataset, and thus allows us to easily make statements about the entire dataset and all its triples. The relationship between a void:Dataset instance and the concrete triples contained in the dataset is established through access information, such as the address of a SPARQL endpoint where the triples can be accessed. #Fields we could include from FAIR #fields taken from fair #dcterms:isPartOf IRI*; #fdp-o:metadataIssued xsd:dateTime; #fdp-o:metadataModified xsd:dateTime; #dcterms:issued xsd:dateTime*; #dcterms:modified xsd:dateTime*; # dcterms:rights IRI*; #dcterms:conformsTo IRI*; #fdp-o:metadataIdentifier @:metadataID; # dcterms:publisher @:agent+;; #dcat:landingPage IRI*; #dcat:theme IRI+; #dcat:keyword xsd:string*; #Links to distribution 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 sapp:ENZDP likelihoodscore xsd:Float; #* The maximum bit score obtained maxbitscore xsd:Float; #* The pattern used pattern xsd:string*; 1 1 1 1 1 1 1 1 1 1 1 1 1 sapp:HMM FSevalue xsd:Double; FSscore xsd:Double; FSbias xsd:Double; TDdomainNumber xsd:Integer; TDdomainsTotal xsd:Integer; TDcevalue xsd:Double; TDievalue xsd:Double; TDscore xsd:Double; TDbias xsd:Double; HMMlocation @:Location; ALIlocation @:Location; ENVlocation @:Location; accuracy xsd:Double; 1 1 1 1 1 1 1 sapp:InterProScanModels #* The accession id of the entry referenced accession xsd:string?; name xsd:string?; #* An optional short description description xsd:string?; key xsd:string?; #* Reference to other entries holding entries with related information in other databases xref @:XRef*; 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 sapp:SignalP #* SignalP properties cMax xsd:Float; #* SignalP properties cPos @:Base; #* SignalP properties yMax xsd:Float; #* SignalP properties yPos @:Base; #* SignalP properties sMax xsd:Float; #* SignalP properties sPos @:Base; #* SignalP properties sMean xsd:Float; #* SignalP properties d xsd:Float; #* SignalP properties signal xsd:string; #* SignalP properties dMaxCut xsd:Float; #* SignalP properties network xsd:string; 1 1 1 1 1 rdf:Bag rdf:List rdf:Seq owl:Class owl:Thing 1 1 1 1 prov:Activity #* The time at which the activity is started prov:startedAtTime xsd:dateTime?; #* The time at which the activity is ended, if unknown set equal to startedAt. prov:endedAtTime xsd:dateTime?; #* Denote the parent activity that initiated this task prov:wasInformedBy @prov:Activity?; #* Description of each of the Data Sets used prov:used @prov:Entity*; #* Description of each generated data set prov:generated @prov:Entity*; #* The agent which be performed this activity wasAssociatedWith @prov:Agent?; DocumentWiseProv 1 prov:Agent #* Tells that this agent performed something for another agent. For example PFam domain scan actedOnBehalfOf InterproScan or a curator that actedOnBehalfOf the EBI. prov:actedOnBehalfOf @prov:Agent? DocumentWiseProv 1 1 prov:Entity prov:wasAttributedTo prov:wasGeneratedBy #* The annotation activity that created this annotation result prov:wasGeneratedBy @prov:Activity?; #* The agent that performed or initiated the activity that generated this entity prov:wasAttributedTo @prov:Agent?; #* Any entries used as input in the activity that created this entity prov:wasDerivedFrom @prov:Entity* DocumentWiseProv prov:Organization DocumentWiseProv prov:SoftwareAgent DocumentWiseProv 1 foaf:Agent #* A human readable (user) name of the agent foaf:name xsd:string; DocumentWiseProv individual and identifiable entity capable of performing actions edit Used to describe any "agent" related to bibliographic items. Such agents can be persons, organizations or groups of any kind. 1 1 1 1 1 1 foaf:Organization #* The legal name of the organization rov:legalName xsd:string?; #* A homepage for some thing. foaf:homepage xsd:string?; #* Link to logo of organization foaf:logo IRI?; #* mail address use URI scheme (see RFC 2368). foaf:mbox IRI?; #* The phone number of the entity foaf:phone xsd:string?; #* Location to which the organization is based near foaf:based_near xsd:string?; DocumentWiseProv social entity (not necessarily commercial) uniting people into a structured group managing shared means to meet some needs, or to pursue collective goals 1 1 1 1 1 1 1 1 1 1 1 1 1 foaf:Person #* Title of the person (Mr, Mrs, Ms, Dr. etc) foaf:title xsd:string?; #* The first name of the person foaf:firstName xsd:string?; #* The first name of the person foaf:surName xsd:string?; #* The given name of a person foaf:givenName xsd:string?; #* The familyName of the person, preferable use the surName property foaf:familyName xsd:string?; #* A homepage for some thing. foaf:homepage xsd:string?; #* Image of the person use link to image foaf:depiction IRI?; #* mail address use URI scheme (see RFC 2368). foaf:mbox IRI?; #* The phone number of the entity foaf:phone xsd:string?; #* The unique identifier to identify the scientist orcid IRI?; #* The prefix of a name bibo:prefixName xsd:string?; #* The suffix of a name bibo:suffixName xsd:string?; #* Used to name the locality of a publisher, an author, etc. bibo:localityName xsd:string?; DocumentWiseProv If class is the root denote it with ROOT Any childs for the framing can be denoted with prefix:prop1 prefix:prop2 NGTax 2.0 classification provenance of ASV's URL: gitlab.com/wurssb/NG-Tax 2-Aminoadipic acid Aad 2-Aminobutyric acid Abu 6-Aminocaproic acid Acp Afghanistan Afghanistan A location that is somewhere after the given position. 2-Aminoheptanoic acid Ahe 2-Aminoisobutyric acid Aib Alanine A Ala Albania Albania Algeria Algeria alignment to a reference genome within the same genus. align_genus alignment to a transcript from the same species. align_trnscpt alignment to a reference genome within another genus. align_xgenus allelic a (unitary) pseudogene that is stable in the population but importantly it has a functional alternative allele also in the population. i.e., one strain may have the gene, another strain may have the pseudogene. MHC haplotypes have allelic pseudogenes. allotype allotype specimen of opposite sex to the holotype A alpha helix American Samoa American Samoa true X AminoAcidOther Other Andorra Andorra Angola Angola Anguilla Anguilla AnnotationLinkSet AnnotationResult Antarctica Antarctica Antigua and Barbuda Antigua and Barbuda 2-Aminopimelic acid Apm Arctic Ocean Arctic Ocean Arginine R Arg Argentina Argentina Armenia Armenia Aruba Aruba Ashmore and Cartier Islands Ashmore and Cartier Islands Asparagine N Asn Aspartic acid D Asp (Aspartate) The gap must be denoted with a series of N's in the sequence, if the assembly gap is of unknown length then number of N must be equal to the estimated length. If that is unknown it default to 100 and so should be denoted with 100 N's in the sequence. No upper or lower limit is set on the size of the gap. Asparagine or Aspartate B Asx Atlantic Ocean Atlantic Ocean attenuator A sequence segment located within the five prime end of an mRNA that causes premature termination of translation. Australia Australia Austria Austria Azerbaijan Azerbaijan Equal to the join in the GenBank format. Unordered set of regions. Bahamas Bahamas Bahrain Bahrain Baker Island Baker Island Baltic Sea Baltic Sea Bangladesh Bangladesh Barbados Barbados Identifies a single base. One-based inclusive same as in GenBank and Faldo 4-acetylcytidine ac4c 5-(carboxyhydroxylmethyl)uridine chm5u 2'-O-methylcytidine cm 5-carboxymethylaminomethyl-2-thiouridine cmnm5s2u 5-carboxymethylaminomethyluridine cmnm5u dihydrouridine dhu 2'-O-methylpseudouridine fm beta-D-galactosylqueuosine gal q 2'-O-methylguanosine gm inosine i N6-isopentenyladenosine i6a 1-methyladenosine m1a 1-methylpseudouridine m1f 1-methylguanosine m1g 1-methylinosine m1i 2,2-dimethylguanosine m22g 2-methyladenosine m2a 2-methylguanosine m2g 3-methylcytidine m3c N4-methylcytosine m4c 5-methylcytidine m5c 5-methyluridine m5u N6-methyladenosine m6a 7-methylguanosine m7g 5-methylaminomethyl-2-thiouridine mam5s2u 5-methylaminomethyluridine mam5u beta-D-mannosylqueuosine man q 5-methoxycarbonylmethyl-2-thiouridine mcm5s2u 5-methoxycarbonylmethyluridine mcm5u 5-methoxyuridine mo5u 2-methylthio-N6-isopentenyladenosine ms2i6a N-((9-beta-D-ribofuranosyl-2-methyltiopurin-6-yl)carbamoyl)threonine ms2t6a N-((9-beta-D-ribofuranosylpurine-6-yl)N-methyl-carbamoyl)threonine mt6a uridine-5-oxoacetic acid methylester mv uridine-5-oxyacetic acid (v) o5u wybutoxosine osyw other base true OTHER pseudouridine p queuosine q 2-thiocytidine s2c 5-methyl-2-thiouridine s2t 2-thiouridine s2u 4-thiouridine s4u t N-((9-beta-D-ribofuranosylpurine-6-yl)carbamoyl)threonine t6a 2'-O-methyl-5-methyluridine tm 2'-O-methyluridine um 3-(3-amino-3-carboxypropyl)uridine, (acp3)u x wybutosine yw Bassas da India Bassas da India A location that is somewhere before the given position. Belarus Belarus Belgian Congo Belgian Congo true Belgium Belgium Belize Belize Benin Benin Bermuda Bermuda A beta strand between scaffolds Bhutan Bhutan Use collection of regions to denote all elements that bind the same element. Bolivia Bolivia Borneo Borneo Bosnia and Herzegovina Bosnia and Herzegovina The feature is located/tells something about both strands. Taken from Faldo ontology Botswana Botswana Bouvet Island Bouvet Island Brazil Brazil British Guiana British Guiana true British Virgin Islands British Virgin Islands Brunei Brunei Bulgaria Bulgaria Burkina Faso Burkina Faso Burma Burma true Burundi Burundi CAAT_signal Part of a conserved sequence located about 75-bp upstream of the start point of eukaryotic transcription units which may be involved in RNA polymerase binding; consensus=GG(C|T)CAATCT. CRISPRCassette A CRISPR repeat Cambodia Cambodia Cameroon Cameroon Canada Canada Cape Verde Cape Verde Use collection of regions to denote all elements of the active side. Cayman Islands Cayman Islands Central African Republic Central African Republic The centromere feature describes the interval of DNA that corresponds to a region where chromatids are held and a kinetochore is formed centromere centromeric_repeat A repeat region found within the modular centromere. Chad Chad Chile Chile China China Christmas Island Christmas Island chromosome_breakpoint A chromosomal region that may sustain a double-strand break, resulting in a recombination event. A circular NA molecule. Clipperton Island Clipperton Island linkage is provided by a clone contig in the tiling path (TPF). For example, a gap where there is a known clone, but there is not yet sequence for that clone. clone_contig Cocos Islands Cocos Islands A coiled coil region A region that is separated over several regions. Ordering of the regions is given by using the the rdfs:_n property. Colombia Colombia satellite Comoros Comoros C_region SequenceFeatureCore constant region of immunoglobulin light and heavy chains, and T-cell receptor alpha, beta, and gamma chains; includes one or more exons depending on the particular chain if any qualifier specified, do not add qualifier put check if qualifier is on transcript or Gene. Possible qualifiers /allele="text"n/citation=[number]n/db_xref="<database>:<identifier>"n/gene="text"n/gene_synonym="text"n/locus_tag="text" (single token)n/map="text"n/note="text"n/old_locus_tag="text" (single token)n/product="text"n/pseudon/pseudogene="TYPE"n/standard_name="text" Cook Islands Cook Islands Coral Sea Islands Coral Sea Islands Costa Rica Costa Rica Cote d'Ivoire Cote d'Ivoire Croatia Croatia The cross links are linked together, so use the location of the other cross link feature to determine location of the partnering base. Cuba Cuba A live microbial or viral culture, or cell lines that have been deposited in curated culture collections. Microbial samples in personal or laboratory collections should be annotated with the strain property. It is implied that the sequence was obtained from a sample retrieved (by the submitter or a collaborator) from the indicated culture collection, or that the sequence was obtained from a sample that was deposited (by the submitter or a collaborator) in the given culture collection. Curacao Curacao Curator Cyprus Cyprus Cysteine C Cys Czech Republic Czech Republic Czechoslovakia Czechoslovakia true DNase_I_hypersensitive_site DNA region representing open chromatin structure that is hypersensitive to digestion by DNase I. 2,4-Diaminobutyric acid Dbu Democratic Republic of the Congo Democratic Republic of the Congo Denmark Denmark Desmosine Des direct A repeat where the same sequence is repeated in the same direction. Example: GCTGA-followed by-GCTGA. dispersed A repeat that is located at dispersed sites in the genome. D_segment SequenceFeatureCore Diversity segment of immunoglobulin heavy chain, andT-cell receptor beta chain; Djibouti Djibouti A preserved domain, domain a typical building blocks of a protein or protein families. Dominica Dominica Dominican Republic Dominican Republic A double stranded RNA molecule 2,2-Diaminopimelic acid Dpm 2,3-Diaminoproprionic acid Dpr East Timor East Timor Ecuador Ecuador Egypt Egypt El Salvador El Salvador enhancer A cis-acting sequence that increases the utilization of (some) eukaryotic promoters, and can function in either orientation and in any location (upstream or downstream) relative to the promoter. enhancer_blocking_element A transcriptional cis regulatory region that when located between an enhancer and a gene's promoter prevents the enhancer from modulating the expression of the gene. Sometimes referred to as an insulator but may not include the barrier function of an insulator. Environmental sampling sequences ENV epitype epitype specimen or illustration selected to serve as an interpretative type when the holotype, lectotype, or previously designated neotype, or all original material associated with a validly published name, cannot be identified for the purpose of the precise application of the name to a taxon Equatorial Guinea Equatorial Guinea Eritrea Eritrea Estonia Estonia N-Ethylasparagine EtAsn N-Ethylglycine EtGly Ethiopia Ethiopia Europa Island Europa Island ex-type ex-type Default Position type, points to an exactly known position. 'expected_count' is the sum of the posterior probability of each read comes from this transcript over all reads. Because 1) each read aligning to this transcript has a probability of being generated from background noise; 2) RSEM may filter some alignable low quality reads, the sum of expected counts for all transcript are generally less than the total number of reads aligned. Expressed Sequence Tag EST Expression object that has to be defined of type FPKM, RPKM, or raw counts. Should be pointing to only one of the three: exon, transcript or gene. QTL type based on expression data Isoform-level relative abundance in Fragments Per Kilobase of exon model per Million mapped fragments Falkland Islands (Islas Malvinas) Falkland Islands (Islas Malvinas) A preserved protein family, protein families typically span the whole protein. Faroe Islands Faroe Islands All subclasses of FeatureProvenance belong to the extensional part of the GBOL ontology. Each subclass is specific to a tool. Fiji Fiji Finland Finland flanking A repeat lying outside the sequence for which it has functional significance (eg. transposon insertion target sites). Former Yugoslav Republic of Macedonia Former Yugoslav Republic of Macedonia true The feature is located/only tells something about the forward strand. Taken from Faldo ontology 4-Aminobutyric acid (piperidinic acid) FourAbu 4-Hydroxyproline FourHyp France France French Guiana French Guiana French Polynesia French Polynesia French Southern and Antarctic Lands French Southern and Antarctic Lands All Position types that not exactly identify the location This class acts as root object of all the data stored within a GBOL file All databases references by the XREF entities within this LinkSet must be referenced by the target property. GC_signal Gabon Gabon Gambia Gambia N_region SequenceFeatureCore extra nucleotides inserted between rearranged immunoglobulin segments. Gaza Strip Gaza Strip the gene feature describes the interval of DNA that corresponds to a genetic trait or phenotype; the feature is, by definition, not strictly bound to it's positions at the ends; it is meant to represent a region where the gene is located. Use this feature to add a citation to a given (sub)sequence Genome Survey Sequence GSS Georgia Georgia Germany Germany Ghana Ghana Gibraltar Gibraltar Glutamine Q Gln Glorioso Islands Glorioso Islands Glutamic acid (Glutamate) E Glu Glutamine or GLutamate Z Glx Glycine G Greece Greece Greenland Greenland Grenada Grenada Guadeloupe Guadeloupe Guam Guam Guatemala Guatemala Guernsey Guernsey Guinea Guinea Guinea-Bissau Guinea-Bissau Guyana Guyana Haiti Haiti hapanotype hapanotype Heard Island and McDonald Islands Heard Island and McDonald Islands heterochromatin heterogeneous population sequenced High level assembly information CON High Throughput CDNA sequencing HTC High Throughput Genome sequencing HTG Histidine H His holotype holotype single physical example (or illustration) of an organism, known to have been used when the species (or lower-ranked taxon) was formally described Honduras Honduras Hong Kong Hong Kong Howland Island Howland Island Hungary Hungary Hydroxylysine Hyl Iceland Iceland Isodesmosine Ide Isoleucine I Ile imprinting_control_region A regulatory region that controls epigenetic imprinting and affects the expression of target genes in an allele- or parent-of-origin-specific manner. Associated regulatory elements may include differentially methylated regions and non-coding RNAs. Identifies a location between two bases Insertion or Deletion Location is somewhere between the begin and end. India India Indian Ocean Indian Ocean Indonesia Indonesia insertion sequence insertion sequence insulator A regulatory region that 1) when located between a CM and a gene's promoter prevents the CRM from modulating that genes expression and 2) acts as a chromatin boundary element or barrier that can block the encroachment of condensed chromatin from an adjacent region. integron integron inverted The sequence is complementarily repeated on the opposite strand. It is a palindrome, and it may, or may not be hyphenated. Examples: GCTGATCAGC, or GCTGA-----TCAGC. Iran Iran Iraq Iraq Ireland Ireland Isle of Man Isle of Man isosyntype isosyntype duplicate of a syntype isotype isotype term used in nomenclature (duplicate of the holotype) Israel Israel Italy Italy Jamaica Jamaica Jan Mayen Jan Mayen Japan Japan Jarvis Island Jarvis Island Jersey Jersey Johnston Atoll Johnston Atoll J_segment SequenceFeatureCore joining segment of immunoglobulin light and heavy-chains, and T-cell receptor alpha, beta, and gamma chains; Jordan Jordan Juan de Nova Island Juan de Nova Island Kazakhstan Kazakhstan Kenya Kenya Kerguelen Archipelago Kerguelen Archipelago Kingman Reef Kingman Reef Kiribati Kiribati The length of gap can be determined based on the associated location. The sequence at the denoted position must be a series of N's. Korea Korea true Kosovo Kosovo Kuwait Kuwait Kyrgyzstan Kyrgyzstan LINE LINE A dispersed repeat family with many copies, each from 1 to 6 kb long. New elements are generated by retroposition of a transcribed copy. Typically the LINE contains 2 ORF's one of which is reverse transcriptase, and 3'and 5' direct repeats. Laos Laos Latvia Latvia Lebanon Lebanon lectotype lectotype Lesotho Lesotho Leucine L Leu Liberia Liberia Libya Libya Liechtenstein Liechtenstein Line Islands Line Islands A linear NA molecule. used when no linkage is being asserted na Equal to the order in the genbank format. Ordered set of regions. Order is denoted with the rdfs:_n predicate. Lithuania Lithuania If reference is not given it is equal to the reference of the parent RegionOfRegion object or is equal to parent Sequence Object. locus_control_region A DNA region that includes DNAse hypersensitive sites located 5' to a gene that confers the high-level, position-independent, and copy number-dependent expression to that gene. long_terminal_repeat long terminal repeat, a sequence directly repeated at both ends of a defined sequence, of the sort typically found in retroviruses; low-quality sequence region Luxembourg Luxembourg Lysine K Lys MITE MITE A highly repetitive and short (100-500 base pair) transposable element with terminal inverted repeats (TIR) and target site duplication (TSD). MITEs do not encode proteins. Macau Macau Macedonia Macedonia Madagascar Madagascar Malawi Malawi Malaysia Malaysia Maldives Maldives Mali Mali Malta Malta If the start and end time are not known, both can be set equal to the time at which the annotation is committed to the database. linkage asserted using a non-sequence based map such as RH, linkage, fingerprint or optical. map Marshall Islands Marshall Islands Martinique Martinique Mass Genome Annotation MGA matrix_attachment_region A DNA region that is required for the binding of chromatin to the nuclear matrix. The location does not include the stop codon (unlike the corresponding CDS) Mauritania Mauritania Mauritius Mauritius Mayotte Mayotte N-Methylglycine (sarcosine) MeGly N-Methylisoleucine MeIle 6-N-Methyllysine MeLys N-Methylvaline MeVal Mediterranean Sea Mediterranean Sea An example entry for assembly information meiotic A genomic region in which there is an exchange of genetic material as a result of the repair of meiosis-specific double strand breaks that occur during meiotic prophase. Methionine M Met QTL type based on metabolite data Mexico Mexico microsatellite A repeat_region containing repeat_units of 2 to 10 bp repeated in tandem. Micronesia Micronesia Midway Islands Midway Islands minisatellite A repeat region containing tandemly repeated sequences having a unit length of 10 to 40 bp. -10_signal minus_10_signal A conserved region about 10-bp upstream of the start point of bacterial transcription units which may be involved in binding RNA polymerase; consensus=TAtAaT. This region is associated with sigma factor 70. -12_signal minus_12_signal A conserved region about 12-bp upstream of the start point of bacterial transcription units, involved with sigma factor 54. -35_signal minus_35_signal A conserved hexamer about 35-bp upstream of the start point of bacterial transcription units; consensus=TTGACa or TGTTGACA. This region is associated with sigma factor 70. note that featureKey regulatory with /regulatory_class="ribosome_binding_site"should be used for ribosome binding sites. This key should not be used when the need is merely to mark a region in order to comment on it or to use it in another feature's location the misc_difference featureKey should be used to describe variability that arises as a result of genetic manipulation (e.g. site directed mutagenesis); use /replace="" to annotate deletion, e.g.misc_difference 412..433/replace="" mitotic value is limited to the restricted vocabulary for modified base abbreviations; Moldova Moldova Monaco Monaco Mongolia Mongolia Montenegro Montenegro Montserrat Montserrat Morocco Morocco Mozambique Mozambique Myanmar Myanmar Physical nucleotide sequence can be a DNA or RNA molecule being either single or double stranded. Represents a physical nucleotide sequence Namibia Namibia used to describe alleles, RFLP's,and other naturally occurring mutations and polymorphisms; variability arising as a result of genetic manipulation (e.g. site directed mutagenesis) should be described with the misc_difference feature;use /replace="" to annotate deletion, e.g.variation 4..5 /replace="" Nauru Nauru Navassa Island Navassa Island neotype neotype neotype strain neotype strain Nepal Nepal nested Netherlands Netherlands Netherlands Antilles Netherlands Antilles true New Caledonia New Caledonia New Zealand New Zealand Nicaragua Nicaragua Niger Niger Nigeria Nigeria Niue Niue Norleucine Nle non-LTR retrotransposon non_ltr_retrotransposon_polymeric_tract A polymeric tract, such as poly(dA), within a non_LTR_retrotransposon. non_allelic_homologous A genomic region at a non-allelic position where exchange of genetic material happens as a result of homologous recombination. Norfolk Island Norfolk Island North Korea North Korea North Sea North Sea Northern Mariana Islands Northern Mariana Islands Norway Norway Note Norvaline Nva Oman Oman Ornithine Orn true Any collection that is not culture collection and not a specimen vouchers collection. other true other true misc_signal other pcr Pacific Ocean Pacific Ocean paired sequences from the two ends of a DNA fragment. paired-ends Pakistan Pakistan Palau Palau Palmyra Atoll Palmyra Atoll Panama Panama Papua New Guinea Papua New Guinea Paracel Islands Paracel Islands Paraguay Paraguay paralectotype paralectotype paratype paratype The sequence within a gap is equal to N The sequence is filled with N for the estimated length otherwise a sequence of 100 N's are included Patent PAT Peru Peru Phenylalanine F Phe Philippines Philippines Pitcairn Islands Pitcairn Islands Poland Poland polyA_signal polyA_signal_sequence The recognition sequence necessary for endonuclease cleavage of an RNA transcript that is followed by polyadenylation; consensus=AATAAA. Portugal Portugal For nucleotide sequences positions always counting always from 5 prime to 3 prime and for protein from n terminal to 5 terminal. Counting is one-based inclusive. used for RNA which may be the result of post-transcriptional processing; if the RNA in question is known not to have been processed, use theprim_transcript key. Used to annotate the site on a given sequence to which a primer molecule binds - not intended to represent the sequence of the primer molecule itself Proline P Pro processed the pseudogene has arisen by reverse transcription of a mRNA into cDNA, followed by reintegration into the genome. Therefore, it has lost any intron/exon structure, and it might have a pseudo-polyA-tail. promoter a region of DNA that initiates transcription of a particular gene The IRI of a sequence of must be equal to http://gbol.life/0.1/protein/<SHA-384 key of protein sequence>. note that featureKey regulatory with /regulatory_class="ribosome_binding_site"should be used for ribosome binding sites. QTL type based on protein data Provenance Mapping tools provenance information true unknown the submitter does not know the method of pseudogenisation. This class can also describe converted GenBank or EMBL entries that have been published Puerto Rico Puerto Rico Pyrrolysine O Pyl QTLMap Qatar Qatar The origin point the entity you which the qualifier belong, such a LinkSet or AnnotationResult. Whereas the provenance point to the supporting evidence of the qualifier Qualifier Restriction Fragment Length Polymorphism RNase_MRP_RNA RNA molecule essential for the catalytic activity of RNase MRP, an enzymatically active ribonucleoprotein with two distinct roles in eukaryotes. In mitochondria it plays a direct role in the initiation of mitochondrial DNA replication, while in the nucleus it is involved in precursor rRNA processing. RNase_P_RNA RNA component of Ribonuclease P (RNase P), a ubiquitous endoribonuclease. The rank can either be defined rank, or can be an undefined rank. If undefined please use the 'Level' enumeration values. Level 1 is the highest level, which is most likely to be equal to 'Kingdom'. class The taxonomic rank: class family The taxonomic rank: family forma The taxonomic rank: forma genus The taxonomic rank: genus infra class The taxonomic rank: infra class infra order The taxonomic rank: infra order kingdom The taxonomic rank: kingdom Rank Level 1 Exact rank unknown: rank level 1 Rank Level 10 Exact rank unknown: rank level 10 Rank Level 11 Exact rank unknown: rank level 11 Rank Level 12 Exact rank unknown: rank level 12 Rank Level 13 Exact rank unknown: rank level 13 Rank Level 14 Exact rank unknown: rank level 14 Rank Level 15 Exact rank unknown: rank level 15 Rank Level 16 Exact rank unknown: rank level 16 Rank Level 17 Exact rank unknown: rank level 17 Rank Level 18 Exact rank unknown: rank level 18 Rank Level 19 Exact rank unknown: rank level 19 Rank Level 2 Exact rank unknown: rank level 2 Rank Level 20 Exact rank unknown: rank level 20 Rank Level 21 Exact rank unknown: rank level 21 Rank Level 22 Exact rank unknown: rank level 22 Rank Level 23 Exact rank unknown: rank level 23 Rank Level 24 Exact rank unknown: rank level 24 Rank Level 25 Exact rank unknown: rank level 25 Rank Level 26 Exact rank unknown: rank level 26 Rank Level 27 Exact rank unknown: rank level 27 Rank Level 28 Exact rank unknown: rank level 28 Rank Level 3 Exact rank unknown: rank level 3 Rank Level 4 Exact rank unknown: rank level 4 Rank Level 5 Exact rank unknown: rank level 5 Rank Level 6 Exact rank unknown: rank level 6 Rank Level 7 Exact rank unknown: rank level 7 Rank Level 8 Exact rank unknown: rank level 8 Rank Level 9 Exact rank unknown: rank level 9 order The taxonomic rank: order parv order The taxonomic rank: parv order phylum The taxonomic rank: phylum species The taxonomic rank: species species group The taxonomic rank: species group species sub group The taxonomic rank: species sub group sub class The taxonomic rank: sub class sub family The taxonomic rank: sub family sub genus The taxonomic rank: sub genus sub kingdom The taxonomic rank: sub kingdom sub order The taxonomic rank: sub order sub phylum The taxonomic rank: sub phylum sub species The taxonomic rank: sub species sub tribe The taxonomic rank: sub tribe super class The taxonomic rank: super class super family The taxonomic rank: super family super kingdom The taxonomic rank: super kingdom super order The taxonomic rank: super order super phylum The taxonomic rank: super phylum tribe The taxonomic rank: tribe varietas The taxonomic rank: variates recoding_stimulatory_region A site in an mRNA sequence that stimulates the recoding of a region in the same mRNA. true other reference strain reference strain The begin position comes always first then the the end position. So for a gene on the reverse complementary strain the begin position is equal to the stop position. We use the same positioning definition as in GenBank and Faldo. This feature has replaced the following Feature Keys on 15-DEC-2014: enhancer, promoter, CAAT_signal, TATA_signal, -35_signal, -10_signal, RBS, GC_signal, polyA_signal, attenuator, terminator, misc_signal. repeat between scaffolds true other /direction has valid values: RIGHT, LEFT, or BOTH. replication_regulatory_region A regulatory region that is involved in the control of the process of nucleotide replication. Republic of the Congo Republic of the Congo response_element A regulatory element that acts in response to a stimulus, usually via transcription factor binding. retro transposon Reunion Reunion The feature is located/only tells something about the reverse strand. Taken from Faldo ontology RBS ribosome_binding_site A region in the 5' UTR that pairs with the 16S rRNA during formation of the preinitiation complex. riboswitch A riboswitch is a part of an mRNA that can act as a direct sensor of small molecules to control their own expression. A riboswitch is a cis element in the 5' end of an mRNA, that acts as a direct sensor of metabolites. Romania Romania Ross Sea Ross Sea Russia Russia Rwanda Rwanda SINE SINE A repetitive element, a few hundred base pairs long, that is dispersed throughout the genome. A common human SINE is the Alu element. true Single Nucleotide Polymorphism SRP_RNA signal recognition particle, a universally conserved ribonucleoprotein involved in the co-translational targeting of proteins to membranes. Simple Sequence Repeat Saint Helena Saint Helena Saint Kitts and Nevis Saint Kitts and Nevis Saint Lucia Saint Lucia Saint Pierre and Miquelon Saint Pierre and Miquelon Saint Vincent and the Grenadines Saint Vincent and the Grenadines Samoa Samoa San Marino San Marino Sao Tome and Principe Sao Tome and Principe Saudi Arabia Saudi Arabia Selenocysteine U Sec Senegal Senegal Physical sequence can be a DNA, RNA or Protein molecule An assembly is defined by list of parts that can either be included sequences or gaps. If a sequence is include a region of the included sequence must be specified. If a gap is include a known or estimated gap length must be specified, if unknown the gap length defaults to 100. The sequence at the gaps is equal to N. The provenance of the assembly process can be included. STS location to include primer(s) in primer_bind key or primers. Sequence Tagged Site STS Serine S Ser Serbia Serbia Serbia and Montenegro Serbia and Montenegro true Seychelles Seychelles short arm Siam Siam true Sierra Leone Sierra Leone silencer A regulatory region which upon binding of transcription factors, suppress the transcription of the gene or genes they control. Singapore Singapore A single stranded DNA molecule A single stranded RNA molecule Sint Maarten Sint Maarten Slovakia Slovakia Slovenia Slovenia Solomon Islands Solomon Islands Somalia Somalia Transgenic sequences can have parts that have another source. South Africa South Africa South Georgia and the South Sandwich Islands South Georgia and the South Sandwich Islands South Korea South Korea South Sudan South Sudan Southern Ocean Southern Ocean Spain Spain A physical specimen that remains after the sequence has been obtained. If the specimen was destroyed in the process of sequencing, electronic images (e-vouchers) are an adequate substitute for a physical voucher specimen. Ideally the specimens will be deposited in a curated museum, herbarium, or frozen tissue collection, but often they will remain in a personal or laboratory collection for some time before they are deposited in a curated collection. Spratly Islands Spratly Islands Sri Lanka Sri Lanka all entries not classified as any of the other classifications Standard true STD true Standard QTL type mapped with genome data State of Palestine State of Palestine Enumeration value that specifies on which strand the element can be found. strobe sequencing (PacBio). strobe Sudan Sudan Suriname Suriname Svalbard Svalbard Swaziland Swaziland Sweden Sweden S_region SequenceFeatureCore switch region of immunoglobulin heavy chains involved in the rearrangement of heavy chain DNA leading to the expression of a different immunoglobulin class from the same B-cell; Switzerland Switzerland syntype syntype Syria Syria TATA_box TATA_signal A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T). termination codon * TERM Transcripts Per Million Taiwan Taiwan Tajikistan Tajikistan tandem Two or more adjacent copies of a region (of length greater than 1). Tanzania Tanzania Tasman Sea Tasman Sea telomere The telomere feature describes the interval of DNA that corresponds to a specific structure at the end of the linear eukaryotic chromosome which is required for the integrity and maintenance of the end; this region is unique compared to the rest of the chromosome and represent the physical end of the chromosome; telomeric_repeat The telomeric repeat is a repeat region, part of the chromosome, which in yeast, is a G-rich terminal sequence of the form (TG(1-3))n or more precisely ((TG)(1-6)TG(2-3))n. Use this class to describe temporary files that contain only information from another prov:Entity, but is formatted differently. Temporary files are typically generated to create files with the correct format for the different tools and output of these tools that need to be converted back. terminal A repeat at the ends of and within the sequence for which it has functional significance other than long terminal repeat. terminator The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription. Thailand Thailand Third PArty sequence data record TPA Threonine T Thr 3-Hydroxyproline ThreeHyp Togo Togo Tokelau Tokelau Tonga Tonga transcriptional_cis_regulatory_region A regulatory region that modulates the transcription of a gene or genes. Transcriptome Shotgun Assembly TSA rep_origin should be used for origins of replication; /direction has legal values RIGHT, LEFT and BOTH, however only RIGHT and LEFT are valid when used in conjunction with the oriT feature; origins of transfer can be present in the chromosome;plasmids can contain multiple origins of transfer transposon Trinidad and Tobago Trinidad and Tobago Tromelin Island Tromelin Island Tryptophan W Trp Tunisia Tunisia Turkey Turkey Turkmenistan Turkmenistan Turks and Caicos Islands Turks and Caicos Islands A turn Tuvalu Tuvalu type material type material type strain type strain the living or permanently preserved culture which is the nomenclatural type of a species or infraspecific taxon Tyrosine Y Tyr USA USA USSR USSR true Uganda Uganda Ukraine Ukraine unitary the pseudogene has no parent. It is the original gene, which is functional in some species but disrupted in some way (indels, mutation, recombination) in another species or strain. United Arab Emirates United Arab Emirates United Kingdom United Kingdom true If the country is unknown. true unkown The gap must be denoted with a series of N's in the sequence, if the assembly gap is of unknown length then number of N must be equal to the estimated length. If that is unknown it default to 100 and so should be denoted with 100 N's in the sequence. No upper or lower limit is set on the size of the gap. unprocessed the pseudogene has arisen from a copy of the parent gene by duplication followed by accumulation of random mutation. The changes, compared to their functional homologue, include insertions, deletions, premature stop codons, frame-shifts and a higher proportion of non-synonymous versus synonymous substitutions. used only when converting old AGPs that lack a field for linkage evidence into the new format. true unspecified a small region of sequenced bases, generally 10 or fewer in its length, which could not be confidently identified. Such a region might contain called bases(A, T, G, or C), or a mixture of called-bases and uncalled-bases ('N').The unsure feature should not be used when annotating gaps in genome assemblies.Please refer to assembly_gap feature for gaps within the sequence of an assembled genome. For annotation of gaps in other sequences than assembled genomes use the gap feature. *Note as observed in GCA_000018045 the unsure region can be larger* use /replace="" to annotate deletion, e.g. unsure 11..15 /replace="" /replace="" is used to annotate deletion, e.g.old_sequence 12..15/replace=""NOTE: This featureKey is not valid in entries/recordscreated from 15-Oct-2007. Uruguay Uruguay Uzbekistan Uzbekistan Valine V Val Vanuatu Vanuatu V_region SequenceFeatureCore variable region of immunoglobulin light and heavychains, and T-cell receptor alpha, beta, and gammachains; codes for the variable amino terminal portion;can be composed of V_segments, D_segments, N_regions,and J_segments; V_segment SequenceFeatureCore variable segment of immunoglobulin light and heavychains, and T-cell receptor alpha, beta, and gammachains; codes for most of the variable region (V_region)and the last few amino acids of the leader peptide; Variation Venezuela Venezuela Viet Nam Viet Nam Virgin Islands Virgin Islands Wake Island Wake Island Wallis and Futuna Wallis and Futuna West Bank West Bank Western Sahara Western Sahara Whole Genome Shotgun WGS sequence on both sides of the gap is derived from the same clone, but the gap is not spanned by paired-ends. The adjacent sequence contigs have unknown order and orientation. within_clone x_element_combinatorial_repeat An X element combinatorial repeat is a repeat region located between the X element and the telomere or adjacent Y' element. XRefProvenance Any amino acid X Xaa Isoleucine or Leucine J Xle y_prime_element A Y' element is a repeat region (SO:0000657) located adjacent to telomeric repeats or X element combinatorial repeats, either as a single copy or tandem repeat of two to four copies. Y_RNA component of the Ro ribonucleoprotein particle (Ro RNP), in association with Ro60 and La proteins. Yemen Yemen Yugoslavia Yugoslavia true Zaire Zaire true Zambia Zambia Zimbabwe Zimbabwe allo-Hydroxylysine aHyl allo-Isoleucine aIle antisense_RNA RNA molecule that is transcribed from the coding, rather than the template, strand of DNA and that is therefore complementary to mRNA. autocatalytically_spliced_intron A self spliced intron. self-splicing intron 3-Aminoadipic acid bAad 3-Aminoisobutyric acid bAib beta-Alanine (beta-Aminoproprionic acid) bAla For QTLs with basepairs as Map Unit For QTLs with centiMorgan as Map Unit guide_RNA short 3'-uridylated RNA that can form a duplex with a stretch of mature edited mRNA hammerhead_ribozyme small catalytic RNA motif that catalyzes a self-cleavage reaction. Its name comes from its secondary structure which resembles a carpenter's hammer. The hammerhead ribozyme is involved in the replication of some viroid and satellite RNAs. the full binomial scientific name of the host organism should be used when known; extra conditional information relating tothe host may also be included lncRNA long non-coding RNA; such molecules are generally defined as having a length greater than 200bp and do not fit into any other ncRNA class. miRNA small, ~22-nt, RNA molecule, termed microRNA, produced from precursor molecules that can form local hairpin structures, which ordinarily are processed (via the Dicer pathway) such that a single miRNA molecule accumulates from one arm of a hairpin precursor molecule. MicroRNAs may trigger the cleavage of their target molecules or act as translational repressors. the ncRNA feature is not used for ribosomal and transferRNA annotation, for which the rRNA and tRNA featureKeysshould be used, respectively; true ncRNATypeOther ncRNA_class not included in any other term. piRNA small RNA molecule, termed Piwi-interacting RNA, expressed in testes and forming RNA-protein complex with Piwi protein; purification of these complexes has revealed that Piwi-interacting RNA oligonucleotides are approximately 24-32 nucleotides long rRNA sizes should be annotated with the /product qualifier. rasiRNA small interfering RNA of length between 17 and 28 nucleotides, derived from the transcript of a repetitive element. ribozyme ribonucleic acid enzyme, RNA molecule that can catalyze specific biochemical reactions. scRNA small cytoplasmic RNA; any one of several small cytoplasmic RNA molecules present in the cytoplasm and (sometimes) nucleus of a eukaryote. siRNA small RNA molecule that is the product of a longer exogenous or endogenous double stranded RNA, which is either a bimolecular duplex or very long hairpin, processed (via the Dicer pathway) such that numerous siRNAs accumulate from both strands of the double stranded RNA. sRNAs trigger the cleavage of their target molecules. snRNA small nuclear RNA molecules involved in pre-mRNA splicing and processing. snoRNA small [nuclear] RNA molecules involved in modification and processing of ribosomal RNA or transfer RNA; found in archaea and in eukaryotic species where they are localized in the nucleolus. telomerase_RNA RNA component of telomerase, a reverse transcriptase that synthesizes telomeric DNA. vault_RNA RNA component of the vault ribonucleo protein, a complex which consists of a major vault protein (MVP), two minor vault proteins (VPARP and TEP1), and several small RNA molecules and has been suggested to be involved in drug resistance. A scholarly academic article, typically published in a journal. Academic Article A written composition in prose, usually nonfiction, on a specific topic, forming an independent part of a book or other publication, as a newspaper or magazine. Article An audio document; aka record. audio document An audio-visual document; film, video, and so forth. audio-visual document Draft legislation presented for discussion to a legal body. Bill A written or printed work of fiction or nonfiction, usually on sheets of paper fastened or bound together within covers. Book A section of a book. Book Section A written argument submitted to a court. Brief A chapter of a book. Chapter A collection of statutes. Code A document that simultaneously contains other documents. Collected Document A collection of Documents or Collections Collection A meeting for consultation or discussion. Conference A collection of legal cases. Court Reporter A document (noun) is a bounded physical representation of body of information designed with the capacity (and usually intent) to communicate. A document may manifest symbolic, diagrammatic or sensory-representational information. Document a distinct part of a larger document or collected document. document part The status of the publication of a document. Document Status An edited book. Edited Book A written communication addressed to a person or organization and transmitted electronically. EMail A passage selected from a larger work. Excerpt aka movie. Film An instance or a session in which testimony and arguments are presented, esp. before an official, as a judge in a lawsuit. Hearing A document that presents visual or diagrammatic information. Image A formalized discussion between two or more people. Interview something that is printed or published and distributed, esp. a given number of a periodical Issue A periodical of scholarly journal Articles. Journal A document accompanying a legal case. Legal Case Document A document containing an authoritative determination (as a decree or judgment) made after consideration of facts or law. Decision A legal document; for example, a court decision, a brief, and so forth. Legal Document A legal document proposing or enacting a law or a group of laws. Legislation A written or printed communication addressed to a person or organization and usually transmitted by mail. Letter Literature A periodical of magazine Articles. A magazine is a publication that is issued periodically, usually bound in a paper cover, and typically contains essays, stories, poems, etc., by many writers, and often photographs and drawings, frequently specializing in a particular subject or area, as hobbies, news, or sports. Magazine A small reference book, especially one giving instructions. Manual An unpublished Document, which may also be submitted to a publisher for publication. Manuscript A graphical depiction of geographic features. Map A loose, thematic, collection of Documents, often Books. Multivolume Book A periodical of documents, usually issued daily or weekly, containing current news, editorials, feature articles, and usually advertising. Newspaper Notes or annotations about a resource. Note A document describing the exclusive right granted by a government to an inventor to manufacture, use, or sell an invention for a certain number of years. Patent A public performance. Performance A group of related documents issued at regular intervals. Periodical A communication between an agent and one or more specific recipients. Personal Communication A personal communication manifested in some document. Personal Communication Document A compilation of documents published from an event, such as a conference. Proceedings An excerpted collection of words. Quote A document that presents authoritative reference information, such as a dictionary or encyclopedia . Reference Source A document describing an account or statement describing in detail an event, situation, or the like, usually as the result of observation, inquiry, etc.. Report A loose, thematic, collection of Documents, often Books. Series A slide in a slideshow Slide A presentation of a series of slides, usually presented in front of an audience with written text and images. Slideshow A document describing a standard Standard A bill enacted into law. Statute A document created to summarize research findings associated with the completion of an academic degree. Thesis The academic degree of a Thesis Thesis degree A web page is an online document available (at least initially) on the world wide web. A web page is written first and foremost to appear on the web, as distinct from other online resources such as books, manuscripts or audio documents which use the web primarily as a distribution mechanism alongside other more traditional methods such as print. Webpage A group of Webpages accessible on the Web. Website A seminar, discussion group, or the like, that emphasizes exchange of ideas and the demonstration and application of techniques, skills, etc. Workshop A legal decision that affirms a ruling. Critical or explanatory note for a Document. annotates The date on which a legal case is argued before a court. Date is of format xsd:date date argued An ordered list of authors. Normally, this list is seen as a priority list that order authors by importance. list of authors An chapter number chapter Relates a document to another document that cites the first document. cited by Relates a document to another document that is cited by the first document as reference, comment, review, quotation or for another purpose. cites This property is for a plain-text rendering of the content of a Document. While the plain-text content of an entire document could be described by this property. content An ordered list of contributors. Normally, this list is seen as a priority list that order contributors by importance. list of contributors A court associated with a legal document; for example, that which issues a decision. court The thesis degree. degree A Film director. director Distributor of a document or a collection of documents. distributor The name defining a special edition of a document. Normally its a literal value composed of a version number and words. edition A person having managerial and sometimes policy-making responsibility for the editorial part of a publishing firm or of a newspaper, magazine, or other publication. editor An ordered list of editors. Normally, this list is seen as a priority list that order editors by importance. list of editors An issue number issue An entity responsible for issuing often informally published documents such as press releases, reports, etc. issuer A description (often numeric) that locates an item within a containing document or collection. locator The number of pages contained in a document number of pages The number of volumes contained in a collection of documents (usually a series, periodical, etc.). number of volumes A generic item or document number. Not to be confused with issue number. number The organizer of an event; includes conference organizers, but also government agencies or other bodies that are responsible for conducting hearings. organizer Owner of a document or a collection of documents. owner Ending page number within a continuous page range. page end Starting page number within a continuous page range. page start A string of non-contiguous page spans that locate a Document within a Collection. Example: 23-25, 34, 54-56. For continuous page ranges, use the pageStart and pageEnd properties. pages performer The prefix of a name prefix name Relates a document to an event; for example, a paper to a conference. presented at Relates an event to associated documents; for example, conference to a paper. presents Producer of a document or a collection of documents. producer An agent that receives a communication document. recipient The resource in which another resource is reproduced. A legal decision that reverses a ruling. Relates a review document to a reviewed thing (resource, item, etc.). review of A section number section The abbreviation of a title. short title The publication status of (typically academic) content. status A legal decision on appeal that takes action on a case (affirming it, reversing it, etc.). The suffix of a name suffix name Relates a document to some transcribed original. transcript of Relates a translated document to the original document. translation of A person who translates written document from one language to another. translator Universal Resource Identifier of a document uri A volume number volume masters degree in arts M.A. masters degree in science M.S. PhD degree PhD degree Accepted for publication after peer reviewing. accepted Document drafted draft Document to be published forthcoming Legal document legal A document that is not peer reviewed non peer reviewed The process by which articles are chosen to be included in a refereed journal. An editorial board consisting of experts in the same field as the author review the article and decide if it is authoritative enough for publication. peer reviewed Published document published Rejected for publication after peer reviewing. rejected Unpublished document unpublished NGTax 2.0 classification of ASV's URL: gitlab.com/wurssb/NG-Tax NGTax Aragorn BLAST Modules from SAPP URL: gitlab.com/sapp/Blast Blast Cog InterProScan Phobius Priam Prodigal RNAmmer TMHMM WoLFPSort prov:Person Used to denote a certain entry within an enumeration to be default value. This is commonly 'anyOtherXXX' This annotation property defines the JSON-LD framing Define all properties for a class, which is parsed by Empusa. Define a class a virtual meaning no direct instances should be created of the class The GBOL API code generated from the GBOL owl file GBOL Api life.gbol.GBOLApi GBOLApi 0.1 ASVAssignment #* Number of hits numberHits xsd:Integer; #* Level count levelCount xsd:Integer; #* Ratio ratio xsd:float; # Type type type::TaxonAssignmentType; #* Taxon taxon @:Taxon; AfterPosition #The exact position on or after which the position is somewhere located (5 prime to 3 prime) position xsd:long; LocationCore Missing from the faldo ontology, taken from the genbank format. In Faldo it is supposed to be modeled with a InRange position that has no end attribute. We did not agree with this design in faldo as it does not reflect the semantics. AnnotationLinkSet DocumentWiseProv An annotation result that exist out of a set of XRefs. AnnotationResult #* The annotation activity that created this annotation result prov:wasGeneratedBy @:AnnotationActivity; #*- prov:wasAttributedTo @prov:Agent; DocumentWiseProv AssemblyGap #* The linkage evidence use to link the sequences on both sides linkageEvidence type::LinkageEvidence?; #* The type of the gap gapType type::GapType; true SequenceFeatureCore A gap within the sequence BagOfRegions members @:Region+- LocationCore Taken over from Faldo Base #* The position of the base at @:Position; #* The strand on which it is positioned strand type::StrandPosition?; LocationCore Taken over from the GenBank format and associated ENA tools. BeforePosition #The exact position on or before which the position is somewhere located (5 prime to 3 prime) position xsd:long; LocationCore Missing from the faldo ontology, taken from the GenBank format. In Faldo it is supposed to be modeled with a InRange position that has no begin attribute. We did not agree with this design in faldo as it does not reflect the semantics. BindingSite SequenceFeatureCore Region(s) of the protein that binds some other entity. CRISPRCassette #* The regions that contain a spacer spacer @:Region+; SequenceFeatureCore CatalyticDomain SequenceFeatureCore The regions that form the catalytic region of protein. Centromere centromere SequenceFeatureCore Region of biological interest identified as a centromere and which has been experimentally characterized; CollectionOfRegions #* A set of regions making up a location spreader over multiple regions. The members inherit the reference value from this CollectionOfRegions object. members @:Region+ LocationCore Taken over from Faldo. ComplementaryDNA A double stranded DNA molecule that is a complementary DNA of an RNA molecule. Counts CrossLink #* Link to the other cross link crossLinkTo @:CrossLink-1; #* Textual description of the crosslink type crossLinkType xsd:string?; SequenceFeatureCore A side that covalently cross links to another cross link side TODO: we could make enumeration for cross link types in the future Curator #* The unique identifier to identify the scientist orcid IRI; DocumentWiseProv DoubleStrandedDNA A double stranded DNA molecule EstimatedCounts ExactPosition #* The exact position (5 prime to 3 prime) position xsd:long LocationCore Taken over from the faldo ontology. We include a 'compressed' format which allows for putting directly a xsd:PositiveInteger value within the LocatableObject without using a separate ExactPosition object. Not included the N- and C-TerminalPositidon from Faldo as all positions are counting from the 5' or N terminal site. C-Terminal counting is rarely used and can also be done from N terminal site, if that is not possible its means we have undefined sequence length which is anyhow incomparable. ExpectedCounts Expression #* To which experiment this expression value belongs to experiment @:Experiment; #* Note on the provenance annotation @:ProvenanceApplication; #* Expression value value xsd:Double; #* Expression type expressionType type::ExpressionType; FPKM FeatureProvenance #* Provenance applies to the given properties or the existence of the feature it self (use gbol:Existence), if not defined it all applies to all properties. onProperty IRI*; ElementWiseProv FuzzyPosition true LocationCore GBOLDataSet ROOT :xref :samples :organisms :annotationResults :linkedDataBases :sequences #* All databases that are linked by any of the contained XRefs linkedDataBases @:Database*-1; #* All annotation result within the GBOL data set annotationResults @:AnnotationResult*-1; #* All samples from which the sequence objects are collected samples @:Sample*-1 ; #* All dna objects included within the GBOL data set sequences @:Sequence*-1 ; #* All associated organisms organisms @:Organism*-1; #* The version of the GBOL Data set, increase by 1 for every (set of) update(s) dataSetVersion xsd:Integer; #* Reference to other entries holding entries with related information in other databases xref @:XRef*; #* A list of keyword describing the content of the GBOL data set keywords xsd:string*; #* The type of this GBOLDataSet entryType type::EntryType; #* A set of references associated to the GBOLDataSet references @:Citation*; #* A set off some additional notes note @:Note*; DocumentCore A complete annotation record stored in GBOL file GBOLLinkSet #* The set of database that are target of the references associated to this link set target @:Database+ DocumentWiseProv Describes and contains the dataset-wise provenance of a set of XREF elements within a GBOLDataSet. Gene :exon #Gene specific things #* All exons that are part of the gene exon @:Exon*; #* All introns that are part of the gene intron @:Intron*; #* All transcripts that are derived from the gene transcript @:Transcript*; #* List of names of known allele variants of the gene allele xsd:string*; #Text #* Symbol of the gene (not the symbol of the resulting protein) geneSymbol xsd:string?; #* Alternative/old gene symbols geneSymbolSynonym xsd:string*; #* If this gene is a pseudo gene, indicate the type pseudogene type::PseudoGeneType?; #* Locus tag of the gene locusTag xsd:string; #* Old locus tag of the gene oldLocusTag xsd:string?; #Text gene SequenceFeatureCore A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions. GeneralFeature SequenceFeatureCore General feature used to add general notes InBetween #* The base after which the in between two bases location is located after @:Position; #* The strand on which it is positioned strand type::StrandPosition?; LocationCore Faldo also has a before property, but as before is equal to after + 1 we removed this property. InRangePosition #The exact position on or after which the position is somewhere located (5 prime to 3 prime) beginPosition xsd:long; #The exact position on or before which the position is somewhere located (5 prime to 3 prime) endPosition xsd:long; LocationCore Taken over from the faldo ontology as it is. KnownLengthAssemblyGap assembly_gap SequenceFeatureCore gap with known gap size between two components of a genome or transcriptome assembly; ListOfRegions members @:Region+= LocationCore Taken over from Faldo Location #* Optionally define another reference sequence then the parent sequence object, this is for example needed for the mdg4 gene of Drosophila, which is transcript from two chromosomes. If the element to which the location belongs is defined on multiple sequence objects, this field is obligatory. referenceSequence @:Sequence? LocationCore We put the reference property in the LocatableObject class and not in the Position class as in the Faldo ontology. A position within sequence A and within sequence B does not make any sense, it is possible to determine what's in between, therefore the reference should be on the region object. However a region can be collection of other regions spread over different reference sequences, such as the mdg4 gene of Drosophila. ManualAnnotationActivity #* - wasAssociatedWith @:Curator?; DocumentWiseProv A manual curation activity MaturePeptide mat_peptide SequenceFeatureCore Mature peptide or protein, after completion of the post-translational modifications. MegaHit #* Note on the provenance provenanceNote xsd:string?; MiscBinding misc_binding SequenceFeatureCore Site in nucleic acid which covalently or non-covalently binds another moiety that cannot be described by any other binding key (primer_bind or protein_bind); MiscFeature misc_feature SequenceFeatureCore Region of biological interest which cannot be described by any other featureKey; a new or rare feature; MiscVariation misc_difference SequenceFeatureCore Any variation other then a natural or an updated sequence variation. ModifiedBase #* The type of modification modBase type::BaseType; #* If applicable, the biological process in which this modification is involved. Use a Biological Process from the GO ontology. modificationFunction IRI?; modified_base SequenceFeatureCore The indicated nucleotide is a modified nucleotide and should be substituted for by the indicated molecule(given in the mod_base qualifier value) NASequence #* The topology of the sequence (linear, circular) topology type::Topology?; #* The set of features annotating the sequence feature @:NAFeature*; #* The translation table of the nucleotide sequence, if not present its inherited from the parent NASequence translTable xsd:PositiveInteger?; #* Indicates that this sequence is obtained from a virus or phage that is integrated into the genome of another organism proviral xsd:boolean?; #* If a clone library was used for sequencing, the sequence can originate from one or more clones clone xsd:string*; #* If a clone library was used for sequencing, specify the clone library cloneLib xsd:string?; #* Indicates if the sequence has undergone somatic rearrangement as part of an adaptive immune response. If equal to false it is the un-rearranged sequence that was inherited from the parental germ line. If equal to true the sequence has undergone somatic rearrangement as part of an adaptive immune response. If not defined it is not applicable to the sequence or unknown. rearranged xsd:boolean?; #* If this NA object is integrated into another NA object, for example a phage genome which is integrated into a bacterial genome or a plasmid which is integrated into a yeast genome. integratedInto @:NASequence?; #* Indicates that this sequence from the macro-nuclear DNA from an organism which undergoes chromosomal differentiation between macro-nuclear and micro-nuclear stages. macronuclear xsd:boolean?; #* Expression feature expression @:Expression*; SequenceFeatureCore NaturalVariation #* The frequency of this variation within the population frequency xsd:Double? variation SequenceFeatureCore A related sequence or allele contains stable mutations from the same gene (e.g., RFLPs, polymorphisms, etc.) which differ from the parent sequence at the given location; NonLTRRetrotransposon non-LTR retrotransposon A retrotransposon without long terminal repeat sequences. Normalised Note #* The textual description of the note text xsd:string; #* The provenance of the feature provenance @:Provenance; DocumentCore PartGap true SequenceFeatureCore A gap within the assembly PartGapUnknownLength SequenceFeatureCore #* The estimated gap length, if not given its unknown and defaults to 100 estimatedLength xsd:PositiveInteger?; A gap within the assembly with unknown sequence length Position LocationCore Counting same as in Faldo and Genbank. PrecursorRNA precursor_RNA prim_transcript SequenceFeatureCore any RNA species that is not yet the mature RNA product, which needs to be described;may have associated transcripts. PrimerBinding #* A textual description of the PCR conditions needed for this primer PCRConditions xsd:string? primer_bind SequenceFeatureCore Non-covalent primer binding site for initiation of replication, transcription, or reverse transcription;includes site(s) for synthetic e.g., PCR primer elements; PCR components and reaction times maybe stored under the "/PCR_conditions" qualifier; since PCR reactions most often involve pairs of primers,a single primer_bind key may use the order() operator with two locations, or a pair of primer_bind keys may be used. Protein #* The set of features annotating the sequence feature @:ProteinFeature*; SequenceFeatureCore Represents any protein sequence ProteinBinding protein_bind SequenceFeatureCore non-covalent protein binding site on nucleic acid; Provenance :annotation #* Note on the provenance annotation @:ProvenanceApplication?; #* Link to the data-wise provenance origin @:AnnotationResult; ElementWiseProv Capturing element wise provenance, hold reference to data-wise provenance ProvenanceMapping ElementWiseProv PublishedGBOLDataSet :dblinks #* The abstract of the publication abstract xsd:string?; #* Cross references to other databases containing the same record dblinks @:XRef*; #* The last time the this GBOL data has been published lastPublishedDate xsd:date?; #* The version of the version that has been last published lastPublishedRelease xsd:Integer?; #* The date at which the record was first published firstPublic xsd:date?; #* The version of the record when it was first published firstPublicRelease xsd:Integer?; #* The date until which the GBOL dataset should not published (only present on non public entries) holddate xsd:date?; #* A free string to keep track of the release status (for private use, not present on public entries) releaseStatus xsd:string?; DocumentCore A GBOLDataSet that has been published QTLMap #* Name of the map the QTL were mapped on mapName xsd:string?; #* Unique map accession Identifier mapAccession xsd:string?; #* Units used for the mapping e.g. Basepairs, centiMorgan units type::MapUnits; #* Parental strains parent @:Organism*; A map that bundles QTLs which were mapped using the same method Qualifier provenance @:Provenance; ElementWiseProv RPKM Rank DocumentCore The rank of a taxonomy RawCounts fwdReadCounts xsd:Double?; revReadCounts xsd:Double?; Region #* The begin position comes always first then the the end position. So for a gene on the reverse complementary strain the begin position is equal to the stop position. We use the same positioning definition as in GenBank and Faldo. begin @:Position; #* The begin position comes always first then the the end position. So for a gene on the reverse complementary strain the begin position is equal to the stop position. We use the same positioning definition as in GenBank and Faldo. end @:Position; #* The strand on which it is positioned strand type::StrandPosition?; LocationCore RegulationSite #*The type of regulation regulatoryClass type::RegulatoryClass?; regulatory SequenceFeatureCore Any region of sequence that functions in the regulation of transcription or translation; type class created, only present in the RegulationSite feature RepeatWithinScaffoldGap repeat within scaffold ReplicationOrigin #* The direction of the replication can be forward, reverse or both replicationDirection type::StrandPosition?; rep_origin SequenceFeatureCore Origin of replication; starting site for duplication of nucleic acid to give two identical copies; Retrotransposon retro transposon Sequence :feature - :Exon #* The hash key of the sequence sha384 xsd:string; #* The sequence, encoded with the default DNA or protein encoding sequence xsd:string; #* The optional assembly information of the sequence assembly @:SequenceAssembly?; #* Length of the sequence length xsd:long; #* The set of features annotating the sequence feature @:Feature*; #* Sample from which this piece of sequence originates from. sample @:Sample?; #* The organism from which the sequence originates from organism @:Organism?; #* An optional short description description xsd:string?; #* The common name of the sequence commonName xsd:string?; #* The recommended name of the sequence recommendedName xsd:string?; #* The standard name of the feature standardName xsd:string?; #* The short name of the sequence shortName xsd:string?; #* The accession id of the entry referenced accession xsd:string*; #* Any alternative names of the sequence alternativeNames xsd:string*; #* Short description of the function function xsd:string?; #* Any publication associated to feature annotation citation @:Citation*; #* The version of the sequence sequenceVersion xsd:PositiveInteger?; #* Reference to other entries holding entries with related information in other databases xref @:XRef*; #* A set off some additional notes note @:Note*; true SequenceFeatureCore Represents a physical sequence SequenceAssembly #* Sorted list of parts that upon concatenation forms the complete sequence. sequencePart @:SequencePart+=; #* The provenance of the feature provenance @:Provenance?; SequenceFeatureCore An assembly of a sequence based on other sequences. SequenceTaggedSite STS SequenceFeatureCore Sequence tagged site; short, single-copy DNA sequence that characterizes a mapping landmark on the genome and can be detected by PCR; a region of the genome can be mapped by determining the order of a series of STS; Source #* Sample from which this piece of sequence originates from. sample @:Sample?; #* The organism from which the sequence originates from organism @:Organism?; source SequenceFeatureCore Indicate other sample source of the sequence then associated to the sequence object. transgenic sequences must have at least two source featurekeys; in a transgenic sequence the source featureKeydescribing the organism that is the recipient of the DNAmust span the entire sequence;see Appendix III /organelle for a list of <organelle_value> StrandPosition LocationCore In Faldo this is a position object, strand is not a Position to which the begin, end or position property can point to. Therefore we defined as a separate type. TPM Telomere telomere SequenceFeatureCore Region of biological interest identified as a telomere and which has been experimentally characterized; TemporaryFile #*- prov:wasDerivedFrom @prov:Entity DocumentWiseProv A temporary file, which is derived from another prov:Entity TransferOrigin oriT SequenceFeatureCore Origin of transfer; region of a DNA molecule where transfer is initiated during the process of conjugation or mobilization #* The direction of the transfer, can be forward or reverse, which effect the direction of the integrated dna strand. transferDirection type::Direction?; Transposon transposon UnknownLengthAssemblyGap #* The estimated gap length, if not given its unknown and defaults to 100 estimatedLength xsd:PositiveInteger?; gap SequenceFeatureCore gap of unknown length in the sequence UnsureBases unsure SequenceFeatureCore A small region of sequenced bases, which could not be confidently identified. UpdatedSequence #* The functional name compare IRI; #@:NASequence old_sequence SequenceFeatureCore The presented variation revises a previous version of the sequence at the given location; Variation #* The type of Variation varType type::VariationTypes; #* Allele of the alternate sequence alternate xsd:string*; #* Quality score of the marker quality xsd:string?; #* Allele of the reference sequence referenceAllele xsd:string?; #* Variant identification code ID xsd:string?; #* filter filter xsd:string?; #* Read depth readDepth xsd:string?; #* Number of Homozygous variant samples homozygousSamples xsd:Integer?; #* Number of Heterozygous variant samples heterozygousSamples xsd:Integer?; #* Number of wildtype samples wildtypeSamples xsd:Integer?; #* Number of samples not called numberNotCalled xsd:Integer?; #* Ancestral Allele ancestralAllele xsd:string?; #* Alelle Count alleleCount xsd:Integer?; #* Frequency in which the alternate allele is found alleleFreq xsd:string?; #* total number of alleles in called genotypes alleleNumber xsd:Integer?; #* RMS base quality baseQuality xsd:string?; #* Cigar string describing alignment of alternate allele to reference CIGAR xsd:string?; #* dbSNP membership dbSNP xsd:string?; #* The begin position comes always first then the the end position. So for a gene on the reverse complementary strain the begin position is equal to the stop position. We use the same positioning definition as in GenBank and Faldo. end @:Position?; #* Mapping Quality mapQuality xsd:string?; #* Number of samples with data numberOfSamples xsd:Integer?; #* Strand bias strandBias xsd:string?; #* Validated validated xsd:string?; #* Genotypes of the sample the variant was called on genotype @:VariantGenotype*; Defines a genomic variant WithinScaffoldGap within scaffold XRefProvenance origin @:AnnotationLinkSet; ElementWiseProv Used to denote the letter used in a protein sequence for the amino acids The label as used in the GenBank and EMBL formats This property marks all the classes that are specific for a tool, marking this class as not belonging to the core of gbol hiseq hiseq2000 hiseq3000 hiseq4000 hiseqx hiseqx_five hiseqx_ten illumina lab_host Scientific name of the laboratory host used to propagate the source organism from which the sample was obtained. The full binomial scientific name of the host organism should be used when known. Extra conditional information relating to the host may also be included. For example '12 year old human with IBD' for a gut bacteria. miniseq miseq miseqdx miseqfgx ncRNA #* The type of the non coding RNA ncRNAClass type::ncRNAType; #* Short description of the product resulting from the feature product xsd:string?; ncRNA SequenceFeatureCore a non-protein-coding gene, other than ribosomal RNA and transfer RNA, the functional molecule of which is the RNAtranscript; /ncRNA_class="miRNA"/ncRNA_class="siRNA"/ncRNA_class="scRNA" nextseq nextseq500 nextseq550 novaseq novaseq600 The parent rank of the rank rRNA #* Short description of the product resulting from the feature product xsd:string?; rRNA SequenceFeatureCore mature ribosomal RNA; RNA component of the ribonucleo protein particle (ribosome) which assembles amino acids into proteins. Define to which sub domain the class belongs, we have separated the GBOL ontology into multiple sub domains bibo:AcademicArticle BIBO http://purl.org/ontology/bibo/ bibo:Article BIBO http://purl.org/ontology/bibo/ bibo:AudioDocument BIBO http://purl.org/ontology/bibo/ bibo:AudioVisualDocument bibo:director @foaf:Agent*; BIBO http://purl.org/ontology/bibo/ bibo:Bill BIBO http://purl.org/ontology/bibo/ bibo:Book BIBO http://purl.org/ontology/bibo/ bibo:BookSection bibo:chapter xsd:string?; BIBO http://purl.org/ontology/bibo/ bibo:Brief BIBO http://purl.org/ontology/bibo/ bibo:Chapter BIBO http://purl.org/ontology/bibo/ bibo:Code bibo:hasPart @bibo:Legislation+; BIBO http://purl.org/ontology/bibo/ bibo:CollectedDocument bibo:hasPart @bibo:Document+; BIBO http://purl.org/ontology/bibo/ bibo:Collection bibo:hasPart @bibo:Literature*; bibo:numVolumes xsd:string?; bibo:eissn xsd:string?; bibo:issn xsd:string?; BIBO http://purl.org/ontology/bibo/ Properties a defined on the root, this is just a temporary note that can be used for that task #bibo:distributor @foaf:Agent?; #bibo:editor @foaf:Agent?; #bibo:issuer @foaf:Agent?; #bibo:owner @foaf:Agent?; #bibo:producer @foaf:Agent?; #bibo:translator @foaf:Agent?; #bibo:doi xsd:string?; #bibo:eissn xsd:string?; #bibo:issn xsd:string?; #bibo:asin xsd:string?; #bibo:identifier xsd:string?; #bibo:coden xsd:string?; #bibo:eanucc13 xsd:string?; #bibo:gtin14 xsd:string?; #bibo:handle xsd:string?; #bibo:isbn10 xsd:string?; #bibo:isbn13 xsd:string?; #bibo:lccn xsd:string?; #bibo:numVolumes xsd:string?; #bibo:oclcnum xsd:string?; #bibo:pmid xsd:string?; #bibo:sici xsd:string?; #bibo:upc xsd:string?; #bibo:uri xsd:string?; bibo:Conference BIBO http://purl.org/ontology/bibo/ bibo:CourtReporter bibo:hasPart @bibo:LegalDocument+; BIBO http://purl.org/ontology/bibo/ bibo:Document BIBO http://purl.org/ontology/bibo/ bibo:DocumentPart BIBO http://purl.org/ontology/bibo/ bibo:DocumentStatus DocumentCore http://purl.org/ontology/bibo/ bibo:EditedBook BIBO http://purl.org/ontology/bibo/ bibo:Email BIBO http://purl.org/ontology/bibo/ bibo:Excerpt BIBO http://purl.org/ontology/bibo/ bibo:Film BIBO http://purl.org/ontology/bibo/ bibo:Hearing BIBO http://purl.org/ontology/bibo/ bibo:Image BIBO http://purl.org/ontology/bibo/ bibo:Interview BIBO http://purl.org/ontology/bibo/ bibo:Issue bibo:hasPart @bibo:Article+; bibo:issue xsd:string?; BIBO http://purl.org/ontology/bibo/ bibo:Journal bibo:hasPart @bibo:Issue+; BIBO http://purl.org/ontology/bibo/ bibo:LegalCaseDocument BIBO http://purl.org/ontology/bibo/ bibo:LegalDecision bibo:affirmedBy @bibo:LegalDecision?; bibo:subsequentLegalDecision @bibo:LegalDecision?; bibo:reversedBy @bibo:LegalDecision?; BIBO http://purl.org/ontology/bibo/ bibo:LegalDocument bibo:court @foaf:Organization; bibo:argued xsd:date; BIBO http://purl.org/ontology/bibo/ bibo:Legislation BIBO http://purl.org/ontology/bibo/ bibo:Letter BIBO http://purl.org/ontology/bibo/ bibo:Literature bibo:asin xsd:string?; bibo:authorList @foaf:Agent*~; bibo:citedBy @bibo:Document*; bibo:cites @bibo:Document*; bibo:coden xsd:string?; bibo:content xsd:string?; bibo:contributorList @foaf:Agent*~; bibo:distributor @foaf:Agent?; bibo:doi xsd:string?; bibo:eanucc13 xsd:string?; bibo:edition xsd:string?; bibo:editor @foaf:Agent?; bibo:editorList @foaf:Agent*~; bibo:gtin14 xsd:string?; bibo:handle xsd:string?; bibo:identifier xsd:string?; bibo:isbn10 xsd:string?; bibo:isbn13 xsd:string?; bibo:issuer @foaf:Agent?; bibo:lccn xsd:string?; bibo:locator xsd:string?; bibo:number xsd:string?; bibo:numPages xsd:Integer?; bibo:oclcnum xsd:string?; bibo:owner @foaf:Agent?; bibo:pageEnd xsd:string?; bibo:pageStart xsd:string?; bibo:pages xsd:string?; bibo:pmid xsd:string?; bibo:presentedAt @bibo:Event?; bibo:producer @foaf:Agent?; bibo:reproducedIn @bibo:Document*; bibo:reviewOf @bibo:Literature*; bibo:section xsd:string?; bibo:shortDescription xsd:string?; bibo:shortTitle xsd:string?; bibo:sici xsd:string?; bibo:status @bibo:DocumentStatus?; bibo:transcriptOf @bibo:Literature?; bibo:translationOf @bibo:Document?; bibo:translator @foaf:Agent?; bibo:upc xsd:string?; bibo:uri xsd:string?; bibo:volume xsd:string?; dc:abstract xsd:string?; dc:contributor @foaf:Agent*; dc:created xsd:date?; dc:description xsd:string?; dc:format @dc:MediaTypeOrExtent?; dc:issued xsd:dateTime?; dc:language xsd:string?; dc:publisher @foaf:Organization?; dc:relation IRI*; dc:rights xsd:string?; dc:subject xsd:string?; dc:title xsd:string?; dc:dateAccepted xsd:dateTime?; dc:dateSubmitted xsd:dateTime?; #* Used in describing structured values. rdf:value xsd:string?; true BIBO bibo:Magazine bibo:hasPart @bibo:Issue+; BIBO http://purl.org/ontology/bibo/ bibo:Manual BIBO http://purl.org/ontology/bibo/ bibo:Manuscript BIBO http://purl.org/ontology/bibo/ bibo:Map BIBO http://purl.org/ontology/bibo/ bibo:MultiVolumeBook bibo:hasPart @bibo:Book*; BIBO http://purl.org/ontology/bibo/ bibo:Newspaper bibo:hasPart @bibo:Issue+; BIBO http://purl.org/ontology/bibo/ bibo:Note bibo:annotates IRI*; BIBO http://purl.org/ontology/bibo/ bibo:Patent BIBO http://purl.org/ontology/bibo/ bibo:Performance bibo:performer @foaf:Agent*; BIBO http://purl.org/ontology/bibo/ bibo:Periodical BIBO http://purl.org/ontology/bibo/ Error in original BIBO ontology LegalDocument is not an Issue; so removed bibo:hasPart @bibo:Issue+; bibo:PersonalCommunication BIBO http://purl.org/ontology/bibo/ bibo:PersonalCommunicationDocument bibo:recipient @foaf:Agent*; BIBO http://purl.org/ontology/bibo/ bibo:Proceedings BIBO http://purl.org/ontology/bibo/ bibo:Quote BIBO http://purl.org/ontology/bibo/ bibo:ReferenceSource BIBO http://purl.org/ontology/bibo/ bibo:Report BIBO http://purl.org/ontology/bibo/ bibo:Series bibo:hasPart @bibo:Document*; BIBO http://purl.org/ontology/bibo/ bibo:Slide BIBO http://purl.org/ontology/bibo/ bibo:Slideshow bibo:hasPart @bibo:Slide*; BIBO http://purl.org/ontology/bibo/ bibo:Standard BIBO http://purl.org/ontology/bibo/ bibo:Statute BIBO http://purl.org/ontology/bibo/ bibo:Thesis bibo:degree type:bibo:ThesisDegree?; BIBO http://purl.org/ontology/bibo/ bibo:ThesisDegree BIBO http://purl.org/ontology/bibo/ bibo:Webpage BIBO http://purl.org/ontology/bibo/ bibo:Website bibo:hasPart @bibo:Webpage+; BIBO http://purl.org/ontology/bibo/ bibo:Workshop BIBO http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ true bibo:content has been deprecated; we recommend to use "rdf:value" for this purpose. Here is the rational behind this choice: http://www.w3.org/TR/2004/REC-rdf-primer-20040210/#rdfvalue http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ We are not defining, using an enumeration, the range of the bibo:degree to the defined list of bibo:ThesisDegree. We won't do it because we want people to be able to define new degrees if needed by some special use cases. Creating such an enumeration would restrict this to happen. We are not defining, using an enumeration, the range of the bibo:degree to the defined list of bibo:ThesisDegree. We won't do it because we want people to be able to define new degrees if needed by some special use cases. Creating such an enumeration would restrict this to happen. http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ The prefix of a name http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ Di Rado, Alicia. 1995. Trekking through college: Classes explore modern society using the world of Star trek. Los Angeles Times, March 15, sec. A, p. 3. http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ We are not defining, using an enumeration, the range of the bibo:status to the defined list of bibo:DocumentStatus. We won't do it because we want people to be able to define new status if needed by some special use cases. Creating such an enumeration would restrict this to happen. We are not defining, using an enumeration, the range of the bibo:status to the defined list of bibo:DocumentStatus. We won't do it because we want people to be able to define new status if needed by some special use cases. Creating such an enumeration would restrict this to happen. http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ The suffix of a name http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ http://purl.org/ontology/bibo/ ssb:NGTax #* FastQ set fastQSet xsd:string+; #* Refernce database refdb xsd:string?; #* Forward read length fReadLength xsd:Integer; #* Reverse read length rReadLength xsd:Integer; #* Map file mapFile xsd:string; #* Minimum percentage threshold minPerT xsd:Float; #* Identity level identLvl xsd:float; #* Error correction errorCorr xsd:Integer; #* Chimera ratio chimeraRatio xsd:float; #* Classify ratio classifyRatio xsd:float; #* Mark if more than one markIfMoreThen1 xsd:Boolean; #* Biom file biomFile xsd:string; #* Turtle file ttlFile xsd:string?; #* E-mail email xsd:string?; #* Project project xsd:string?; #* Max chimera distance forward maxChemeraDistF xsd:Integer; #* Max chimera distance reverse maxChemeraDistR xsd:Integer; #* Max clustering mismatch count maxClusteringMismatchCount xsd:Integer; #* Identity 97 mismatch count identity97MismatchCount xsd:Integer; #* Identity 95 mismatch count identity95MismatchCount xsd:Integer; #* Identity 92 mismatch count identity92MismatchCount xsd:Integer; #* Identity 90 mismatch count identity90MismatchCount xsd:Integer; #* Identity 85 mismatch count identity85MismatchCount xsd:Integer; #* Forward primer length fPrimerLength xsd:Integer; #* Reverse primer length rPrimerLength xsd:Integer; #* The Id used, typically typed as a prefix id xsd:string; #* Format format xsd:string; #* Format URL formatURL xsd:string; #* Type headerType xsd:string; #* Generated by generatedBy xsd:string; #* The version of the resource version xsd:string; #* Commit commit xsd:string?; #* Date date xsd:string; #* Matrix type matrixType xsd:string; #* Matrix element type matrixElementType xsd:string; #* Folder option folder xsd:string?; #* Mismatch DB mismatchDB xsd:Boolean?; #* Log file logFile xsd:string?; #* Shanon option shanon xsd:Boolean?; #* Rejected ASV Annotation rja xsd:Integer?; #* Minimum size of rejected OTU to be classify minOTUSizeT xsd:Integer; sapp:Aragorn Aragorn sapp:Blast #* The percentage identity of a similarity analysis percIdentity xsd:Float?; #* The alignment length of two sequence objects alignmentLength xsd:Integer?; #* The number of mismatches between two sequence objects mismatches xsd:Integer?; #* The nuber of gaps between two sequence objects gaps xsd:Integer?; #* The probability of an alignment evalue xsd:double?; #* The bitscore of an alignment bitscore xsd:Float?; sapp:Cog #* The name of an organism organismName xsd:string?; #* The COG membership class membershipClass xsd:string?; #* The letter of the COG group letter xsd:string?; #* A description of a given object label xsd:string?; #cogInfo @:CogInfo?; COG results obtained through a BLAST approach sapp:InterProScan #* The probability of an alignment evalue xsd:double?; familyName xsd:string?; #* Score given by this method score xsd:double; InterProScan Module from SAPP URL: gitlab.com/sapp/annotation/interproscan sapp:Phobius # Phobius specific properties phobiusType xsd:string; # Phobius specific properties location @:Location; # Phobius specific properties description xsd:string; sapp:Priam # Priam specific properties sourceRegion @:Region; # Priam specific properties profileId xsd:string; # Priam specific properties profileLength xsd:Integer?; # Priam specific properties alignLength xsd:Integer?; # Priam specific properties queryStrand xsd:string?; # Priam specific properties profileRegioin @:Region; # Priam specific properties profileProportion xsd:Float; # Priam specific properties bitScore xsd:Float; #* The probability of an alignment evalue xsd:double?; # Priam specific properties positiveHitProbability xsd:Float; # Priam specific properties isBestOverlap xsd:string; # Priam specific properties foundCatalyticPattern xsd:string; sapp:Prodigal # Prodigal specific properties under FeatureProvenance rbsMotif xsd:string; # Prodigal specific properties startType xsd:string; # Prodigal specific properties rbsSpacer xsd:string; # Prodigal specific properties gcContent xsd:string; # Prodigal specific properties conf xsd:Float; # Prodigal specific properties score xsd:Double; # Prodigal specific properties cScore xsd:Float; # Prodigal specific properties sScore xsd:Float; # Prodigal specific properties rScore xsd:Float; # Prodigal specific properties uScore xsd:Float; # Prodigal specific properties tScore xsd:Float; Prodigal sapp:RNAmmer #* Score given by this method score xsd:double; #* RNAmmer properties attribute xsd:string? RNAmmer sapp:TMHMM #* TMHMM properties location @:Location?; #* Type thmmType xsd:string?; #* The sequence, encoded with the default DNA or protein encoding sequence xsd:string? sapp:WoLFPSort #* Score given by this method score xsd:double; #* subcellular localization of a predicted protein subLocation IRI+ WoLFPSort Module from SAPP URL: gitlab.com/sapp/wolfpsort prov:Person DocumentWiseProv