Usage

Main code.

class DecentralizedBiomedicalOntology(date=<factory>, data_version=None, force=False)[source]

Get the ontology.

ontology: ClassVar[str] = 'debio': The prefix for the ontology

typedefs: ClassVar[Optional[List[TypeDef]]] = [TypeDef(reference=Reference(prefix='debio', identifier='0000001', name='gene product is a member of'), comment=None, namespace=None, definition=None, is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[Reference(prefix='ro', identifier='0002205', name='has gene product'), Reference(prefix='ro', identifier='0002350', name='member of')], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000002', name='has mature miRNA'), comment=None, namespace=None, definition=None, is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000003', name='species specific'), comment=None, namespace=None, definition='X speciesSpecific Y means that Y is a general phenomena, like a pathway, and X is the version that appears in a species. X should state which species with RO:0002162 (in taxon)', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000004', name='Antibody has target'), comment=None, namespace=None, definition=None, is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000006', name='has salt'), comment=None, namespace=None, definition=None, is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000007', name='has left-to-right reaction'), comment=None, namespace=None, definition='X ltr Y means reaction X of undetermined direction has a left-to-right reaction Y. Relevant for Rhea.', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000008', name='has right-to-left reaction'), comment=None, namespace=None, definition='X rtl Y means reaction X of undetermined direction has a right-to-left reaction Y. Relevant for Rhea.', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000009', name='has bi-directional reaction'), comment=None, namespace=None, definition='X bi Y means reaction X of undetermined direction has a bidirectional reaction Y. Relevant for Rhea.', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000010', name='is conjugate base of'), comment=None, namespace=None, definition='X is conjugate base of Y typically means that X is a deprotonated form of Y', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[Reference(prefix='obo', identifier='chebi#is_conjugate_base_of', name=None), Reference(prefix='ro', identifier='0018033', name=None)], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000011', name='is conjugate acid of'), comment=None, namespace=None, definition='X is conjugate acid of Y typically means that Y is a protonated form of X', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[Reference(prefix='obo', identifier='chebi#is_conjugate_acid_of', name=None), Reference(prefix='ro', identifier='0018034', name=None)], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000012', name='is enantiomer of'), comment=None, namespace=None, definition='X and Y are in an enantiomeric relationship if flipping all stereocenters of X results in Y', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[Reference(prefix='obo', identifier='chebi#is_enantiomer_of', name=None), Reference(prefix='ro', identifier='0018039', name=None)], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000013', name='is tautomer of'), comment=None, namespace=None, definition='X and Y are tautomers if they are different realizations of the resonance structure of the same molecule', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[Reference(prefix='obo', identifier='chebi#is_tautomer_of', name=None), Reference(prefix='ro', identifier='0018036', name=None)], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000014', name='has parent hydride'), comment=None, namespace=None, definition='X has parent hydride Y if the substituents on X are replaced with hydrogens. E.g., SbCl3 has parent hydride SbH3', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[Reference(prefix='obo', identifier='chebi#has_parent_hydride', name=None), Reference(prefix='ro', identifier='0018040', name=None)], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000015', name='has functional parent'), comment=None, namespace=None, definition='X has functional parent Y if X is a derivative (e.g., a salt) of Y. E.g., bepridil hydrochloride has functional parent bepridil', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[Reference(prefix='obo', identifier='chebi#has_functional_parent', name=None), Reference(prefix='ro', identifier='0000015', name=None)], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000025', name='has origin'), comment=None, namespace=None, definition='Related to sequences', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[Reference(prefix='obo', identifier='so#has_origin', name=None)], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000027', name='is substituent group from'), comment=None, namespace=None, definition='connects a group to its chemical entity (e.g., carboyxylic acid group to acetate)', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[Reference(prefix='obo', identifier='chebi#is_substituent_group_from', name=None)], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000029', name='has citation'), comment=None, namespace=None, definition='connects any entity to a document (e.g., with a pubmed, doi, pmc, or arxiv identifier)', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000032', name='causes side effect'), comment=None, namespace=None, definition='connects any entity a side effect that it causes. For example, VO:0000112 (Tripedia) induces the side effect HP:0002013 (Vomiting)', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000033', name='pathogen has host'), comment=None, namespace=None, definition='connects a pathogen (NCBITaxon) to a host (NCBITaxon)', is_transitive=None, is_symmetric=None, domain=Reference(prefix='ncbitaxon', identifier='1', name=None), range=Reference(prefix='ncbitaxon', identifier='1', name=None), parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000034', name='vaccine has gene engineering'), comment=None, namespace=None, definition='connects a vaccine (VO) to a gene that has been engineered. Most applicable to OMVs, Nanosponges, and nanolipoparticles (NLP).', is_transitive=None, is_symmetric=None, domain=Reference(prefix='vo', identifier='0000001', name=None), range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000035', name='has intervention'), comment=None, namespace=None, definition='connects a clinical trial to an intervention it investigates', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000036', name='has condition'), comment=None, namespace=None, definition='connects a clinical trial to a condition it investigates', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000037', name='has platform'), comment=None, namespace=None, definition='connects a vaccine to its platform', is_transitive=None, is_symmetric=None, domain=Reference(prefix='vo', identifier='0000001', name=None), range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000038', name='mentioned in'), comment=None, namespace=None, definition="connects any entity to an article in which it's mentioned, e.g., extracted from NER", is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000039', name='annotated with'), comment=None, namespace=None, definition='connects an article to a term it was annotated with (i.e. pubmed annotated with MeSH term)', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000040', name='related trial'), comment=None, namespace=None, definition='connects a related trial registered in a different registry', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000041', name='prevents infection'), comment=None, namespace=None, definition='Sibling relationship to vo:0001011 (immunizes against disease)', is_transitive=None, is_symmetric=None, domain=Reference(prefix='vo', identifier='0000001', name=None), range=Reference(prefix='doid', identifier='4', name=None), parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000044', name='pathogen defines vaccine class'), comment=None, namespace=None, definition='A relationship where the domain is a taxon and the range is a vaccine family. E.g., Severe acute respiratory syndrome coronavirus 2 (ncbitaxon:2697049) is the pathogen that defines vaccine class COVID-19 vaccine (VO:0004908). Sort of an inverse of VO:0003355, but more specific', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000045', name='vector vaccine uses pathogen as vector'), comment=None, namespace=None, definition='connects a vaccine platform that is a vector vaccine to a pathogen that it uses as a vector', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000046', name='search results in'), comment=None, namespace=None, definition='connects any entity to an article that a search over the entity label or its synonyms produces', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0001-9439-5346', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000047', name='reaction enabled by molecular function'), comment=None, namespace=None, definition='connects a reaction (e.g., from Rhea) to a molecular function (e.g., from GO) that corresponds', is_transitive=None, is_symmetric=None, domain=None, range=Reference(prefix='go', identifier='0003674', name=None), parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000048', name='trial occurred in country'), comment=None, namespace=None, definition='connects a trial (e.g., from ClinicalTrials.gov) to a country (e.g., from GeoNames) based on where the trial took place', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000049', name='has active license from'), comment=None, namespace=None, definition='connects a vaccine (e.g., from VO) to a country or organization where it has an active license through standard approval', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000050', name='has active EUA license from'), comment=None, namespace=None, definition='connects a vaccine (e.g., from VO) to a country or organization where it has an active license through emergency use authorization (EUA)', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=None), TypeDef(reference=Reference(prefix='debio', identifier='0000005', name='locus group'), comment=None, namespace=None, definition=None, is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=True), TypeDef(reference=Reference(prefix='debio', identifier='0000016', name='monoisotopic mass'), comment=None, namespace=None, definition=None, is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[Reference(prefix='obo', identifier='chebi/monoisotopicmass', name=None)], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=True), TypeDef(reference=Reference(prefix='debio', identifier='0000017', name='charge'), comment=None, namespace=None, definition=None, is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[Reference(prefix='obo', identifier='chebi/charge', name=None)], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=True), TypeDef(reference=Reference(prefix='debio', identifier='0000018', name='formula'), comment=None, namespace=None, definition=None, is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[Reference(prefix='obo', identifier='chebi/formula', name=None), Reference(prefix='obo', identifier='fbbt#FORMULA', name=None)], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=True), TypeDef(reference=Reference(prefix='debio', identifier='0000019', name='mass'), comment=None, namespace=None, definition=None, is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[Reference(prefix='obo', identifier='chebi/mass', name=None)], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=True), TypeDef(reference=Reference(prefix='debio', identifier='0000020', name='InChI'), comment=None, namespace=None, definition=None, is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[Reference(prefix='obo', identifier='chebi/inchi', name=None), Reference(prefix='obo', identifier='fbbt#InChI', name=None), Reference(prefix='wikidata', identifier='P234', name=None)], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=True), TypeDef(reference=Reference(prefix='debio', identifier='0000021', name='InChI Key'), comment=None, namespace=None, definition=None, is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[Reference(prefix='obo', identifier='chebi/inchikey', name=None), Reference(prefix='obo', identifier='fbbt#InChIKey', name=None), Reference(prefix='wikidata', identifier='P235', name=None)], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=True), TypeDef(reference=Reference(prefix='debio', identifier='0000022', name='smiles'), comment=None, namespace=None, definition=None, is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[Reference(prefix='obo', identifier='chebi/smiles', name=None), Reference(prefix='obo', identifier='fbbt#SMILES', name=None)], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=True), TypeDef(reference=Reference(prefix='debio', identifier='0000023', name='has taxonomy rank'), comment=None, namespace=None, definition=None, is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[Reference(prefix='obo', identifier='ncbitaxon#has_rank', name=None)], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=True), TypeDef(reference=Reference(prefix='debio', identifier='0000024', name='has species group'), comment=None, namespace=None, definition=None, is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[Reference(prefix='obo', identifier='NCBITaxon#_species_group', name=None)], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=True), TypeDef(reference=Reference(prefix='debio', identifier='0000026', name='IUPAC Name'), comment=None, namespace=None, definition=None, is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[Reference(prefix='obo', identifier='chebi#IUPAC_NAME', name=None), Reference(prefix='obo', identifier='fbbt#IUPAC_NAME', name=None)], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=True), TypeDef(reference=Reference(prefix='debio', identifier='0000028', name='International Nonproprietary Name'), comment=None, namespace=None, definition=None, is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[Reference(prefix='obo', identifier='chebi#INN', name=None), Reference(prefix='obo', identifier='fbbt#INN', name=None)], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=True), TypeDef(reference=Reference(prefix='debio', identifier='0000030', name='has related symbol'), comment=None, namespace=None, definition='This term is most applicable to terms appearing in mathematical equations (e.g., rate laws) and connects the base concept to a symbol that has been used to represent it in a synonym.', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[Reference(prefix='oboinowl', identifier='hasRelatedSynonym', name='has related synonym')], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=True), TypeDef(reference=Reference(prefix='debio', identifier='0000031', name='has related LaTeX'), comment=None, namespace=None, definition='This term is most applicable to terms appearing in mathematical equations (e.g., rate laws) and connects the base concept to a the latex representing the symbol that has been used to represent it in a synonym.', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[Reference(prefix='oboinowl', identifier='hasRelatedSynonym', name='has related synonym')], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=True), TypeDef(reference=Reference(prefix='debio', identifier='0000042', name='constant has value'), comment=None, namespace=None, definition='Connects an individual representing a physical constant to its numeric value', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=True), TypeDef(reference=Reference(prefix='debio', identifier='0000043', name='constant has formula'), comment=None, namespace=None, definition='Connects an individual representing a physical constant to its formula', is_transitive=None, is_symmetric=None, domain=None, range=None, parents=[], xrefs=[], inverse=None, created_by='orcid:0000-0003-4423-4370', holds_over_chain=[], is_metadata_tag=True)]: Type definitions

synonym_typedefs: ClassVar[Optional[List[SynonymTypeDef]]] = []: Synonym type definitions

idspaces: ClassVar[Optional[Mapping[str, str]]] = {'RO': 'http://purl.obolibrary.org/obo/RO_', 'debio': 'https://biopragmatics.github.io/debio/', 'obo': 'http://purl.obolibrary.org/obo/', 'orcid': 'https://orcid.org/'}: The idspaces used in the document

data_version: Optional[str] = '0.1.2-dev': The ontology version

iter_terms(force=False)[source]

Iterate over terms in the ontology.

Return type:: Iterable[Term]