Source code for indra.databases.identifiers

import re
import logging
from indra.resources import load_resource_json


logger = logging.getLogger(__name__)


identifiers_url = 'https://identifiers.org'

# These are just special cases of name spaces where the mapping from INDRA to
# identifiers.org is not a question of simplecapitalization.
identifiers_mappings = {
    'UP': 'uniprot',
    'UPPRO': 'uniprot.chain',
    'UPISO': 'uniprot.isoform',
    'REFSEQ_PROT': 'refseq',
    'PF': 'pfam',
    'IP': 'interpro',
    'ECCODE': 'ec-code',
    'NONCODE': 'noncodev4.rna',
    'LNCRNADB': 'rnacentral',
    'MIRBASEM': 'mirbase.mature',
    'EGID': 'ncbigene',
    'NCBI': 'ncibgene',
    'HGNC_GROUP': 'hgnc.genefamily',
    'LINCS': 'lincs.smallmolecule',
    'PUBCHEM': 'pubchem.compound',
    'CHEMBL': 'chembl.compound',
    'CTD': 'ctd.chemical',
    'CVCL': 'cellosaurus',
}

# These are namespaces used by INDRA that don't have corresponding
# identifiers.org entries
non_registry = {
    'SDIS', 'SCHEM', 'SFAM', 'SCOMP', 'SIGNOR', 'HMS-LINCS', 'NXPFA',
    'OMIM', 'LSPCI', 'UPLOC', 'BFO'
}

# These are namespaces that can appear in db_refs but are actually not
# representing grounding.
non_grounding = {
    'TEXT', 'TEXT_NORM'
}

# These are reverse mappings from identifiers.org namespaces to INDRA
# namespaces
identifiers_reverse = {
    v: k for k, v in identifiers_mappings.items()
}
# We have to patch this one because it is ambiguous
identifiers_reverse['ncbigene'] = 'EGID'

# These are only the URLs that are strictly prefixes and not more complicated
# patterns. This is because some downstream code uses these as prefixes
# rather than arbitrary patterns.
url_prefixes = {
    # Biology namespaces
    'NXPFA': 'https://www.nextprot.org/term/FA-',
    'SIGNOR': 'https://signor.uniroma2.it/relation_result.php?id=',
    # WM namespaces
    'UN': 'https://github.com/clulab/eidos/wiki/JSON-LD#Grounding/',
    'WDI': 'https://github.com/clulab/eidos/wiki/JSON-LD#Grounding/',
    'FAO': 'https://github.com/clulab/eidos/wiki/JSON-LD#Grounding/',
    'HUME': ('https://github.com/BBN-E/Hume/blob/master/resource/ontologies'
             '/hume_ontology/'),
    'CWMS': 'http://trips.ihmc.us/',
    'SOFIA': 'http://cs.cmu.edu/sofia/',
}


[docs]def get_ns_from_identifiers(identifiers_ns): """"Return a namespace compatible with INDRA from an identifiers namespace. For example, this function can be used to map 'uniprot' to 'UP'. Parameters ---------- identifiers_ns : str An identifiers.org standard namespace. Returns ------- str or None The namespace compatible with INDRA's internal representation or None if the given namespace isn't an identifiers.org standard. """ reg_entry = identifiers_registry.get(identifiers_ns.lower()) if not reg_entry: return None mapping = identifiers_reverse.get(identifiers_ns.lower()) if mapping: return mapping else: return identifiers_ns.upper()
[docs]def get_ns_id_from_identifiers(identifiers_ns, identifiers_id): """Return a namespace/ID pair compatible with INDRA from identifiers. Parameters ---------- identifiers_ns : str An identifiers.org standard namespace. identifiers_id : str An identifiers.org standard ID in the given namespace. Returns ------- (str, str) A namespace and ID that are valid in INDRA db_refs. """ reg_entry = identifiers_registry.get(identifiers_ns.lower()) db_ns = get_ns_from_identifiers(identifiers_ns) if db_ns is None: return None, None db_id = identifiers_id if reg_entry['namespace_embedded']: if not identifiers_id.startswith(identifiers_ns.upper()): db_id = '%s:%s' % (identifiers_ns.upper(), identifiers_id) return db_ns, db_id
[docs]def get_identifiers_ns(db_name): """Map an INDRA namespace to an identifiers.org namespace when possible. Example: this can be used to map 'UP' to 'uniprot'. Parameters ---------- db_name : str An INDRA namespace to map to identifiers.org Returns ------- str or None An identifiers.org namespace or None if not available. """ mapped_db_name = identifiers_mappings.get(db_name, db_name.lower()) if mapped_db_name not in identifiers_registry: return None return mapped_db_name
[docs]def get_url_prefix(db_name): """Return the URL prefix for a given namespace.""" identifiers_ns = get_identifiers_ns(db_name) if identifiers_ns: identifiers_entry = identifiers_registry.get(identifiers_ns) if not identifiers_entry['namespace_embedded']: return '%s/%s:' % (identifiers_url, identifiers_ns.lower()) else: return '%s/' % identifiers_url else: if db_name in url_prefixes: return url_prefixes[db_name] return None
[docs]def get_identifiers_url(db_name, db_id): """Return an identifiers.org URL for a given database name and ID. Parameters ---------- db_name : str An internal database name: HGNC, UP, CHEBI, etc. db_id : str An identifier in the given database. Returns ------- url : str An identifiers.org URL corresponding to the given database name and ID. """ # This is the case where we have a prefix that we can simply attach the # db_id to to get the desired URL. if db_name == 'CHEMBL': db_id = ensure_chembl_prefix(db_id) elif db_name == 'CHEBI': db_id = ensure_chebi_prefix(db_id) prefix = get_url_prefix(db_name) if prefix: return '%s%s' % (prefix, db_id) # Otherwise, we have to handle some special cases bel_scai_url = 'https://arty.scai.fraunhofer.de/artifactory/bel/namespace/' if db_name == 'LINCS': if db_id.startswith('LSM-'): # Lincs Small Molecule ID url = identifiers_url + '/lincs.smallmolecule:%s' % db_id elif db_id.startswith('LCL-'): # Lincs Cell Line ID url = identifiers_url + '/lincs.cell:%s' % db_id else: # Assume LINCS Protein url = identifiers_url + '/lincs.protein:%s' % db_id elif db_name == 'CHEMBL': if not db_id.startswith('CHEMBL'): db_id = 'CHEMBL%s' % db_id url = identifiers_url + '/chembl.compound:%s' % db_id elif db_name == 'HMS-LINCS': url = 'http://lincs.hms.harvard.edu/db/sm/%s-101' % db_id # Special cases with no identifiers entry elif db_name == 'SCHEM': url = bel_scai_url + 'selventa-legacy-chemicals/' + \ 'selventa-legacy-chemicals-20150601.belns' elif db_name == 'SCOMP': url = bel_scai_url + 'selventa-named-complexes/' + \ 'selventa-named-complexes-20150601.belns' elif db_name == 'SFAM': url = bel_scai_url + 'selventa-protein-families/' + \ 'selventa-protein-families-20150601.belns' elif db_name == 'TEXT' or db_name == 'TEXT_NORM': return None else: logger.warning('Unhandled name space %s' % db_name) url = None return url
[docs]def parse_identifiers_url(url): """Retrieve database name and ID given the URL. Parameters ---------- url : str An identifiers.org URL to parse. Returns ------- db_name : str An internal database name: HGNC, UP, CHEBI, etc. corresponding to the given URL. db_id : str An identifier in the database. """ # Try matching by string pattern db_ns, db_id = None, None url_pattern = \ r'(?:https?)://identifiers.org/([A-Za-z0-9.-]+)(/|:)([A-Za-z0-9:_.-]+)' match = re.match(url_pattern, url) if match is not None: g = match.groups() if len(g) == 3: pattern_ns, pattern_id = g[0], g[2] db_ns, db_id = get_ns_id_from_identifiers(pattern_ns, pattern_id) if db_ns == 'HGNC': if db_id.startswith('HGNC:'): db_id = db_id[5:] # If we got UP and UPPRO, return UPPRO if db_ns == 'UP' and '#PRO_' in url: db_ns = 'UPPRO' db_id = url[url.find('PRO_'):] if db_ns and db_id: return db_ns, db_id for ns, prefix in url_prefixes.items(): if url.startswith(prefix): return ns, url[len(prefix):] # Handle other special cases for part in ['/lincs.smallmolecule', '/lincs.cell', '/lincs.protein']: if part in url: return 'LINCS', url[(url.find(part) + len(part) + 1):] if '/chembl.compound' in url: return 'CHEMBL', url[ (url.find('/chembl.compound') + len('/chembl.compound:')):] if 'lincs.hms.harvard.edu' in url: return 'HMS-LINCS', url[len('http://lincs.hms.harvard.edu/db/sm/'):-4] if 'selventa-legacy-chemicals/' in url: return 'SCHEM', None if 'selventa-named-complexes/' in url: return 'SCOMP', None if 'selventa-protein-families/' in url: return 'SFAM', None else: logger.warning('Could not parse URL %s' % url) return None, None
[docs]def namespace_embedded(db_ns: str) -> bool: """Return true if this namespace requires IDs to have namespace embedded. This function first maps the given namespace to an identifiers.org namespace and then checks the registry to see if namespaces need to be embedded in IDs. If yes, it returns True. If not, or the ID can't be mapped to identifiers.org, it returns False Parameters ---------- db_ns : The namespace to check. Returns ------- : True if the namespace is known to be embedded in IDs of this namespace. False if unknown or known not to be embedded. """ identifiers_ns = get_identifiers_ns(db_ns) if identifiers_ns: identifiers_entry = identifiers_registry.get(identifiers_ns) if identifiers_entry['namespace_embedded']: return True return False
[docs]def ensure_prefix_if_needed(db_ns: str, db_id: str) -> str: """Return an ID ensuring a namespace prefix if known to be needed. Parameters ---------- db_ns : The namespace associated with the identifier. db_id : The original identifier. Returns ------- : The identifier with namespace embedded if needed. """ if namespace_embedded(db_ns): return ensure_prefix(db_ns, db_id) return db_id
[docs]def ensure_prefix(db_ns, db_id, with_colon=True): """Return a valid ID that has the given namespace embedded. This is useful for namespaces such as CHEBI, GO or BTO that require the namespace to be part of the ID. Note that this function always ensures that the given db_ns is embedded in the ID and can handle the case whene it's already present. Parameters ---------- db_ns : str A namespace. db_id : str An ID within that namespace which should have the namespace as a prefix in it. with_colon: Optional[bool] If True, the namespace prefix is followed by a colon in the ID (e.g., CHEBI:12345). Otherwise, no colon is added (e.g., CHEMBL1234). Default: True """ if db_id is None: return None colon = ':' if with_colon else '' if not db_id.startswith(f'{db_ns}{colon}'): return f'{db_ns}{colon}{db_id}' return db_id
[docs]def ensure_chebi_prefix(chebi_id): """Return a valid CHEBI ID that has the appropriate CHEBI: prefix.""" return ensure_prefix('CHEBI', chebi_id)
[docs]def ensure_chembl_prefix(chembl_id): """Return a valid CHEMBL ID that has the appropriate CHEMBL prefix.""" return ensure_prefix('CHEMBL', chembl_id, with_colon=False)
identifiers_registry = load_resource_json('identifiers_patterns.json')