Database clients (indra.databases)

This module implements a number of clients for accessing and using resources from biomedical entity databases and other third-party web services that INDRA uses. Many of the resources these clients use are loaded from resource files in the indra.resources module, in many cases also providing access to web service endpoints.

identifiers.org mappings and URLs (indra.databases.identifiers)

indra.databases.identifiers.ensure_chebi_prefix(chebi_id)

Return a valid CHEBI ID that has the appropriate CHEBI: prefix.

indra.databases.identifiers.ensure_chembl_prefix(chembl_id)

Return a valid CHEMBL ID that has the appropriate CHEMBL prefix.

indra.databases.identifiers.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

indra.databases.identifiers.ensure_prefix_if_needed(db_ns, db_id)

Return an ID ensuring a namespace prefix if known to be needed.

Parameters

• db_ns (str) – The namespace associated with the identifier.

• db_id (str) – The original identifier.

Return type

str

Returns

The identifier with namespace embedded if needed.

indra.databases.identifiers.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

An identifiers.org namespace or None if not available.

Return type

str or None

indra.databases.identifiers.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 – An identifiers.org URL corresponding to the given database name and ID.

Return type

str

indra.databases.identifiers.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

The namespace compatible with INDRA’s internal representation or None if the given namespace isn’t an identifiers.org standard.

Return type

str or None

indra.databases.identifiers.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

A namespace and ID that are valid in INDRA db_refs.

Return type

(str, str)

indra.databases.identifiers.get_url_prefix(db_name)

Return the URL prefix for a given namespace.

indra.databases.identifiers.namespace_embedded(db_ns)

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 (str) – The namespace to check.

Return type

bool

Returns

True if the namespace is known to be embedded in IDs of this namespace. False if unknown or known not to be embedded.

indra.databases.identifiers.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.

HGNC client (indra.databases.hgnc_client)

indra.databases.hgnc_client.get_current_hgnc_id(hgnc_name)

Return HGNC ID(s) corresponding to a current or outdated HGNC symbol.

Parameters

hgnc_name (str) – The HGNC symbol to be converted, possibly an outdated symbol.

Returns

If there is a single HGNC ID corresponding to the given current or outdated HGNC symbol, that ID is returned as a string. If the symbol is outdated and maps to multiple current IDs, a list of these IDs is returned. If the given name doesn’t correspond to either a current or an outdated HGNC symbol, None is returned.

Return type

str or list of str or None

indra.databases.hgnc_client.get_ensembl_id(hgnc_id)

Return the Ensembl ID corresponding to the given HGNC ID.

Parameters

hgnc_id (str) – The HGNC ID to be converted. Note that the HGNC ID is a number that is passed as a string. It is not the same as the HGNC gene symbol.

Returns

ensembl_id – The Ensembl ID corresponding to the given HGNC ID.

Return type

str

indra.databases.hgnc_client.get_entrez_id(hgnc_id)

Return the Entrez ID corresponding to the given HGNC ID.

Parameters

hgnc_id (str) – The HGNC ID to be converted. Note that the HGNC ID is a number that is passed as a string. It is not the same as the HGNC gene symbol.

Returns

entrez_id – The Entrez ID corresponding to the given HGNC ID.

Return type

str

indra.databases.hgnc_client.get_gene_type(hgnc_id)

Return the locus type of the genve with the given HGNC ID.

See more under Locus type at https://www.genenames.org/help/symbol-report/#!/#tocAnchor-1-2

Parameters

hgnc_id (str) – The HGNC ID of the gene to get the locus type of.

Return type

Optional[str]

Returns

The locus type of the given gene.

indra.databases.hgnc_client.get_hgnc_entry(hgnc_id)

Return the HGNC entry for the given HGNC ID from the web service.

Parameters

hgnc_id (str) – The HGNC ID to be converted.

Returns

xml_tree – The XML ElementTree corresponding to the entry for the given HGNC ID.

Return type

ElementTree

indra.databases.hgnc_client.get_hgnc_from_ensembl(ensembl_id)

Return the HGNC ID corresponding to the given Ensembl ID.

Parameters

ensembl_id (str) – The Ensembl ID to be converted, a number passed as a string.

Returns

hgnc_id – The HGNC ID corresponding to the given Ensembl ID.

Return type

str

indra.databases.hgnc_client.get_hgnc_from_entrez(entrez_id)

Return the HGNC ID corresponding to the given Entrez ID.

Parameters

entrez_id (str) – The Entrez ID to be converted, a number passed as a string.

Returns

hgnc_id – The HGNC ID corresponding to the given Entrez ID.

Return type

str

indra.databases.hgnc_client.get_hgnc_from_mouse(mgi_id)

Return the HGNC ID corresponding to the given MGI mouse gene ID.

Parameters

mgi_id (str) – The MGI ID to be converted. Example: “2444934”

Returns

hgnc_id – The HGNC ID corresponding to the given MGI ID.

Return type

str

indra.databases.hgnc_client.get_hgnc_from_rat(rgd_id)

Return the HGNC ID corresponding to the given RGD rat gene ID.

Parameters

rgd_id (str) – The RGD ID to be converted. Example: “1564928”

Returns

hgnc_id – The HGNC ID corresponding to the given RGD ID.

Return type

str

indra.databases.hgnc_client.get_hgnc_id(hgnc_name)

Return the HGNC ID corresponding to the given HGNC symbol.

Parameters

hgnc_name (str) – The HGNC symbol to be converted. Example: BRAF

Returns

hgnc_id – The HGNC ID corresponding to the given HGNC symbol.

Return type

str

indra.databases.hgnc_client.get_hgnc_name(hgnc_id)

Return the HGNC symbol corresponding to the given HGNC ID.

Parameters

hgnc_id (str) – The HGNC ID to be converted.

Returns

hgnc_name – The HGNC symbol corresponding to the given HGNC ID.

Return type

str

indra.databases.hgnc_client.get_mouse_id(hgnc_id)

Return the MGI mouse ID corresponding to the given HGNC ID.

Parameters

hgnc_id (str) – The HGNC ID to be converted. Example: “”

Returns

mgi_id – The MGI ID corresponding to the given HGNC ID.

Return type

str

indra.databases.hgnc_client.get_rat_id(hgnc_id)

Return the RGD rat ID corresponding to the given HGNC ID.

Parameters

hgnc_id (str) – The HGNC ID to be converted. Example: “”

Returns

rgd_id – The RGD ID corresponding to the given HGNC ID.

Return type

str

indra.databases.hgnc_client.get_uniprot_id(hgnc_id)

Return the UniProt ID corresponding to the given HGNC ID.

Parameters

hgnc_id (str) – The HGNC ID to be converted. Note that the HGNC ID is a number that is passed as a string. It is not the same as the HGNC gene symbol.

Returns

uniprot_id – The UniProt ID corresponding to the given HGNC ID.

Return type

str

indra.databases.hgnc_client.is_kinase(gene_name)

Return True if the given gene name is a kinase.

Parameters

gene_name (str) – The HGNC gene symbol corresponding to the protein.

Returns

True if the given gene name corresponds to a kinase, False otherwise.

Return type

bool

indra.databases.hgnc_client.is_phosphatase(gene_name)

Return True if the given gene name is a phosphatase.

Parameters

gene_name (str) – The HGNC gene symbol corresponding to the protein.

Returns

True if the given gene name corresponds to a phosphatase, False otherwise.

Return type

bool

indra.databases.hgnc_client.is_transcription_factor(gene_name)

Return True if the given gene name is a transcription factor.

Parameters

gene_name (str) – The HGNC gene symbol corresponding to the protein.

Returns

True if the given gene name corresponds to a transcription factor, False otherwise.

Return type

bool

Uniprot client (indra.databases.uniprot_client)

ChEBI client (indra.databases.chebi_client)

indra.databases.chebi_client.get_chebi_entry_from_web(chebi_id)

Return a ChEBI entry corresponding to a given ChEBI ID using a REST API.

Parameters

chebi_id (str) – The ChEBI ID whose entry is to be returned.

Returns

An ElementTree element representing the ChEBI entry.

Return type

xml.etree.ElementTree.Element

indra.databases.chebi_client.get_chebi_id_from_cas(cas_id)

Return a ChEBI ID corresponding to the given CAS ID.

Parameters

cas_id (str) – The CAS ID to be converted.

Returns

chebi_id – The ChEBI ID corresponding to the given CAS ID. If the lookup fails, None is returned.

Return type

str

indra.databases.chebi_client.get_chebi_id_from_chembl(chembl_id)

Return a ChEBI ID from a given ChEBML ID.

Parameters

chembl_id (str) – ChEBML ID to be converted.

Returns

chebi_id – ChEBI ID corresponding to the given ChEBML ID. If the lookup fails, None is returned.

Return type

str

indra.databases.chebi_client.get_chebi_id_from_hmdb(hmdb_id)

Return the ChEBI ID corresponding to an HMDB ID.

Parameters

hmdb_id (str) – An HMDB ID.

Returns

The ChEBI ID that the given HMDB ID maps to or None if no mapping was found.

Return type

str

indra.databases.chebi_client.get_chebi_id_from_name(chebi_name)

Return a ChEBI ID corresponding to the given ChEBI name.

Parameters

chebi_name (str) – The ChEBI name whose ID is to be returned.

Returns

chebi_id – The ID corresponding to the given ChEBI name. If the lookup fails, None is returned.

Return type

str

indra.databases.chebi_client.get_chebi_id_from_pubchem(pubchem_id)

Return the ChEBI ID corresponding to a given Pubchem ID.

Parameters

pubchem_id (str) – Pubchem ID to be converted.

Returns

chebi_id – ChEBI ID corresponding to the given Pubchem ID. If the lookup fails, None is returned.

Return type

str

indra.databases.chebi_client.get_chebi_name_from_id(chebi_id, offline=True)

Return a ChEBI name corresponding to the given ChEBI ID.

Parameters

• chebi_id (str) – The ChEBI ID whose name is to be returned.

• offline (Optional[bool]) – If False, the ChEBI web service is invoked in case a name mapping could not be found in the local resource file. Default: True

Returns

chebi_name – The name corresponding to the given ChEBI ID. If the lookup fails, None is returned.

Return type

str

indra.databases.chebi_client.get_chebi_name_from_id_web(chebi_id)

Return a ChEBI name corresponding to a given ChEBI ID using a REST API.

Parameters

chebi_id (str) – The ChEBI ID whose name is to be returned.

Returns

chebi_name – The name corresponding to the given ChEBI ID. If the lookup fails, None is returned.

Return type

str

indra.databases.chebi_client.get_chembl_id(chebi_id)

Return a ChEMBL ID from a given ChEBI ID.

Parameters

chebi_id (str) – ChEBI ID to be converted.

Returns

chembl_id – ChEMBL ID corresponding to the given ChEBI ID. If the lookup fails, None is returned.

Return type

str

indra.databases.chebi_client.get_inchi_key(chebi_id)

Return an InChIKey corresponding to a given ChEBI ID using a REST API.

Parameters

chebi_id (str) – The ChEBI ID whose InChIKey is to be returned.

Returns

The InChIKey corresponding to the given ChEBI ID. If the lookup fails, None is returned.

Return type

str

indra.databases.chebi_client.get_primary_id(chebi_id)

Return the primary ID corresponding to a ChEBI ID.

Note that if the provided ID is a primary ID, it is returned unchanged.

Parameters

chebi_id (str) – The ChEBI ID that should be mapped to its primary equivalent.

Returns

The primary ChEBI ID or None if the provided ID is neither primary nor a secondary ID with a primary mapping.

Return type

str or None

indra.databases.chebi_client.get_pubchem_id(chebi_id)

Return the PubChem ID corresponding to a given ChEBI ID.

Parameters

chebi_id (str) – ChEBI ID to be converted.

Returns

pubchem_id – PubChem ID corresponding to the given ChEBI ID. If the lookup fails, None is returned.

Return type

str

indra.databases.chebi_client.get_specific_id(chebi_ids)

Return the most specific ID in a list based on the hierarchy.

Parameters

chebi_ids (list of str) – A list of ChEBI IDs some of which may be hierarchically related.

Returns

The first ChEBI ID which is at the most specific level in the hierarchy with respect to the input list.

Return type

str

Cell type context client (indra.databases.context_client)

indra.databases.context_client.get_mutations(gene_names, cell_types)

Return protein amino acid changes in given genes and cell types.

Parameters

• gene_names (list) – HGNC gene symbols for which mutations are queried.

• cell_types (list) –

  List of cell type names in which mutations are queried. The cell type names follow the CCLE database conventions.

  Example: LOXIMVI_SKIN, BT20_BREAST

Returns

res – A dictionary keyed by cell line, which contains another dictionary that is keyed by gene name, with a list of amino acid substitutions as values.

Return type

dict[dict[list]]

indra.databases.context_client.get_protein_expression(gene_names, cell_types)

Return the protein expression levels of genes in cell types.

Parameters

• gene_names (list) – HGNC gene symbols for which expression levels are queried.

• cell_types (list) –

  List of cell type names in which expression levels are queried. The cell type names follow the CCLE database conventions.

  Example: LOXIMVI_SKIN, BT20_BREAST

Returns

res – A dictionary keyed by cell line, which contains another dictionary that is keyed by gene name, with estimated protein amounts as values.

Return type

dict[dict[float]]

NDEx client (indra.databases.ndex_client)

indra.databases.ndex_client.create_network(cx_str, ndex_cred=None, private=True)

Creates a new NDEx network of the assembled CX model.

To upload the assembled CX model to NDEx, you need to have a registered account on NDEx (http://ndexbio.org/) and have the ndex python package installed. The uploaded network is private by default.

Parameters

ndex_cred (dict) – A dictionary with the following entries: ‘user’: NDEx user name ‘password’: NDEx password

Returns

network_id – The UUID of the NDEx network that was created by uploading the assembled CX model.

Return type

str

indra.databases.ndex_client.get_default_ndex_cred(ndex_cred)

Gets the NDEx credentials from the dict, or tries the environment if None

indra.databases.ndex_client.send_request(ndex_service_url, params, is_json=True, use_get=False)

Send a request to the NDEx server.

Parameters

• ndex_service_url (str) – The URL of the service to use for the request.

• params (dict) – A dictionary of parameters to send with the request. Parameter keys differ based on the type of request.

• is_json (bool) – True if the response is in json format, otherwise it is assumed to be text. Default: False

• use_get (bool) – True if the request needs to use GET instead of POST.

Returns

res – Depending on the type of service and the is_json parameter, this function either returns a text string or a json dict.

Return type

str

indra.databases.ndex_client.set_style(network_id, ndex_cred=None, template_id=None)

Set the style of the network to a given template network’s style

Parameters

• network_id (str) – The UUID of the NDEx network whose style is to be changed.

• ndex_cred (dict) – A dictionary of NDEx credentials.

• template_id (Optional[str]) – The UUID of the NDEx network whose style is used on the network specified in the first argument.

indra.databases.ndex_client.update_network(cx_str, network_id, ndex_cred=None)

Update an existing CX network on NDEx with new CX content.

Parameters

• cx_str (str) – String containing the CX content.

• network_id (str) – UUID of the network on NDEx.

• ndex_cred (dict) – A dictionary with the following entries: ‘user’: NDEx user name ‘password’: NDEx password

cBio portal client (indra.databases.cbio_client)

indra.databases.cbio_client.get_cancer_studies(study_filter=None)

Return a list of cancer study identifiers, optionally filtered.

There are typically multiple studies for a given type of cancer and a filter can be used to constrain the returned list.

Parameters

study_filter (Optional[str]) – A string used to filter the study IDs to return. Example: “paad”

Returns

study_ids – A list of study IDs. For instance “paad” as a filter would result in a list of study IDs with paad in their name like “paad_icgc”, “paad_tcga”, etc.

Return type

list[str]

indra.databases.cbio_client.get_cancer_types(cancer_filter=None)

Return a list of cancer types, optionally filtered.

Parameters

cancer_filter (Optional[str]) – A string used to filter cancer types. Its value is the name or part of the name of a type of cancer. Example: “melanoma”, “pancreatic”, “non-small cell lung”

Returns

type_ids – A list of cancer types matching the filter. Example: for cancer_filter=”pancreatic”, the result includes “panet” (neuro-endocrine) and “paad” (adenocarcinoma)

Return type

list[str]

indra.databases.cbio_client.get_case_lists(study_id)

Return a list of the case set ids for a particular study.

TAKE NOTE the “case_list_id” are the same thing as “case_set_id” Within the data, this string is referred to as a “case_list_id”. Within API calls it is referred to as a ‘case_set_id’. The documentation does not make this explicitly clear.

Parameters

study_id (str) – The ID of the cBio study. Example: ‘cellline_ccle_broad’ or ‘paad_icgc’

Returns

case_set_ids – A dict keyed to cases containing a dict keyed to genes containing int

Return type

dict[dict[int]]

indra.databases.cbio_client.get_ccle_cna(gene_list, cell_lines)

Return a dict of CNAs in given genes and cell lines from CCLE.

CNA values correspond to the following alterations

-2 = homozygous deletion

-1 = hemizygous deletion

0 = neutral / no change

1 = gain

2 = high level amplification

Parameters

• gene_list (list[str]) – A list of HGNC gene symbols to get mutations in

• cell_lines (list[str]) – A list of CCLE cell line names to get mutations for.

Returns

profile_data – A dict keyed to cases containing a dict keyed to genes containing int

Return type

dict[dict[int]]

indra.databases.cbio_client.get_ccle_lines_for_mutation(gene, amino_acid_change)

Return cell lines with a given point mutation in a given gene.

Checks which cell lines in CCLE have a particular point mutation in a given gene and return their names in a list.

Parameters

• gene (str) – The HGNC symbol of the mutated gene in whose product the amino acid change occurs. Example: “BRAF”

• amino_acid_change (str) – The amino acid change of interest. Example: “V600E”

Returns

cell_lines – A list of CCLE cell lines in which the given mutation occurs.

Return type

list

indra.databases.cbio_client.get_ccle_mrna(gene_list, cell_lines)

Return a dict of mRNA amounts in given genes and cell lines from CCLE.

Parameters

• gene_list (list[str]) – A list of HGNC gene symbols to get mRNA amounts for.

• cell_lines (list[str]) – A list of CCLE cell line names to get mRNA amounts for.

Returns

mrna_amounts – A dict keyed to cell lines containing a dict keyed to genes containing float

Return type

dict[dict[float]]

indra.databases.cbio_client.get_ccle_mutations(gene_list, cell_lines, mutation_type=None)

Return a dict of mutations in given genes and cell lines from CCLE.

This is a specialized call to get_mutations tailored to CCLE cell lines.

Parameters

• gene_list (list[str]) – A list of HGNC gene symbols to get mutations in

• cell_lines (list[str]) – A list of CCLE cell line names to get mutations for.

• mutation_type (Optional[str]) – The type of mutation to filter to. mutation_type can be one of: missense, nonsense, frame_shift_ins, frame_shift_del, splice_site

Returns

mutations – The result from cBioPortal as a dict in the format {cell_line : {gene : [mutation1, mutation2, …] }}

Example: {‘LOXIMVI_SKIN’: {‘BRAF’: [‘V600E’, ‘I208V’]}, ‘SKMEL30_SKIN’: {‘BRAF’: [‘D287H’, ‘E275K’]}}

Return type

dict

indra.databases.cbio_client.get_genetic_profiles(study_id, profile_filter=None)

Return all the genetic profiles (data sets) for a given study.

Genetic profiles are different types of data for a given study. For instance the study ‘cellline_ccle_broad’ has profiles such as ‘cellline_ccle_broad_mutations’ for mutations, ‘cellline_ccle_broad_CNA’ for copy number alterations, etc.

Parameters

• study_id (str) – The ID of the cBio study. Example: ‘paad_icgc’

• profile_filter (Optional[str]) – A string used to filter the profiles to return. Will be one of: - MUTATION - MUTATION_EXTENDED - COPY_NUMBER_ALTERATION - MRNA_EXPRESSION - METHYLATION The genetic profiles can include “mutation”, “CNA”, “rppa”, “methylation”, etc.

Returns

genetic_profiles – A list of genetic profiles available for the given study.

Return type

list[str]

indra.databases.cbio_client.get_mutations(study_id, gene_list, mutation_type=None, case_id=None)

Return mutations as a list of genes and list of amino acid changes.

Parameters

• study_id (str) – The ID of the cBio study. Example: ‘cellline_ccle_broad’ or ‘paad_icgc’

• gene_list (list[str]) – A list of genes with their HGNC symbols. Example: [‘BRAF’, ‘KRAS’]

• mutation_type (Optional[str]) – The type of mutation to filter to. mutation_type can be one of: missense, nonsense, frame_shift_ins, frame_shift_del, splice_site

• case_id (Optional[str]) – The case ID within the study to filter to.

Returns

mutations – A tuple of two lists, the first one containing a list of genes, and the second one a list of amino acid changes in those genes.

Return type

tuple[list]

indra.databases.cbio_client.get_num_sequenced(study_id)

Return number of sequenced tumors for given study.

This is useful for calculating mutation statistics in terms of the prevalence of certain mutations within a type of cancer.

Parameters

study_id (str) – The ID of the cBio study. Example: ‘paad_icgc’

Returns

num_case – The number of sequenced tumors in the given study

Return type

int

indra.databases.cbio_client.get_profile_data(study_id, gene_list, profile_filter, case_set_filter=None)

Return dict of cases and genes and their respective values.

Parameters

• study_id (str) – The ID of the cBio study. Example: ‘cellline_ccle_broad’ or ‘paad_icgc’

• gene_list (list[str]) – A list of genes with their HGNC symbols. Example: [‘BRAF’, ‘KRAS’]

• profile_filter (str) – A string used to filter the profiles to return. Will be one of: - MUTATION - MUTATION_EXTENDED - COPY_NUMBER_ALTERATION - MRNA_EXPRESSION - METHYLATION

• case_set_filter (Optional[str]) – A string that specifices which case_set_id to use, based on a complete or partial match. If not provided, will look for study_id + ‘_all’

Returns

profile_data – A dict keyed to cases containing a dict keyed to genes containing int

Return type

dict[dict[int]]

indra.databases.cbio_client.send_request(**kwargs)

Return a data frame from a web service request to cBio portal.

Sends a web service requrest to the cBio portal with arguments given in the dictionary data and returns a Pandas data frame on success.

More information about the service here: http://www.cbioportal.org/web_api.jsp

Parameters

kwargs (dict) – A dict of parameters for the query. Entries map directly to web service calls with the exception of the optional ‘skiprows’ entry, whose value is used as the number of rows to skip when reading the result data frame.

Returns

df – Response from cBioPortal as a Pandas DataFrame.

Return type

pandas.DataFrame

ChEMBL client (indra.databases.chembl_client)

indra.databases.chembl_client.activities_by_target(activities)

Get back lists of activities in a dict keyed by ChEMBL target id

Parameters

activities (list) – response from a query returning activities for a drug

Returns

targ_act_dict – dictionary keyed to ChEMBL target ids with lists of activity ids

Return type

dict

indra.databases.chembl_client.get_chembl_id(nlm_mesh)

Get ChEMBL ID from NLM MESH

Parameters

nlm_mesh (str) –

Returns

chembl_id

Return type

str

indra.databases.chembl_client.get_chembl_name(chembl_id)

Return a standard ChEMBL name from an ID if available in the local resource.

Parameters

chembl_id (str) – The ChEBML ID to get the name for.

Returns

The corresponding ChEBML name or None if not available.

Return type

str or None

indra.databases.chembl_client.get_drug_inhibition_stmts(drug)

Query ChEMBL for kinetics data given drug as Agent get back statements

Parameters

drug (Agent) – Agent representing drug with MESH or CHEBI grounding

Returns

stmts – INDRA statements generated by querying ChEMBL for all kinetics data of a drug interacting with protein targets

Return type

list of INDRA statements

indra.databases.chembl_client.get_evidence(assay)

Given an activity, return an INDRA Evidence object.

Parameters

assay (dict) – an activity from the activities list returned by a query to the API

Returns

ev – an Evidence object containing the kinetics of the

Return type

Evidence

indra.databases.chembl_client.get_kinetics(assay)

Given an activity, return its kinetics values.

Parameters

assay (dict) – an activity from the activities list returned by a query to the API

Returns

kin – dictionary of values with units keyed to value types ‘IC50’, ‘EC50’, ‘INH’, ‘Potency’, ‘Kd’

Return type

dict

indra.databases.chembl_client.get_mesh_id(nlm_mesh)

Get MESH ID from NLM MESH

Parameters

nlm_mesh (str) –

Returns

mesh_id

Return type

str

indra.databases.chembl_client.get_pcid(mesh_id)

Get PC ID from MESH ID

Parameters

mesh (str) –

Returns

pcid

Return type

str

indra.databases.chembl_client.get_pmid(doc_id)

Get PMID from document_chembl_id

Parameters

doc_id (str) –

Returns

pmid

Return type

str

indra.databases.chembl_client.get_protein_targets_only(target_chembl_ids)

Given list of ChEMBL target ids, return dict of SINGLE PROTEIN targets

Parameters

target_chembl_ids (list) – list of chembl_ids as strings

Returns

protein_targets – dictionary keyed to ChEMBL target ids with lists of activity ids

Return type

dict

indra.databases.chembl_client.get_target_chemblid(target_upid)

Get ChEMBL ID from UniProt upid

Parameters

target_upid (str) –

Returns

target_chembl_id

Return type

str

indra.databases.chembl_client.query_target(target_chembl_id)

Query ChEMBL API target by id

Parameters

target_chembl_id (str) –

Returns

target – dict parsed from json that is unique for the target

Return type

dict

indra.databases.chembl_client.send_query(query_dict)

Query ChEMBL API

Parameters

query_dict (dict) – ‘query’ : string of the endpoint to query ‘params’ : dict of params for the query

Returns

js – dict parsed from json that is unique to the submitted query

Return type

dict

LINCS client (indra.databases.lincs_client)

class indra.databases.lincs_client.LincsClient

Client for querying LINCS small molecules and proteins.

get_protein_refs(hms_lincs_id)

Get the refs for a protein from the LINCs protein metadata.

Parameters

hms_lincs_id (str) – The HMS LINCS ID for the protein

Returns

A dictionary of protein references.

Return type

dict

get_small_molecule_name(hms_lincs_id)

Get the name of a small molecule from the LINCS sm metadata.

Parameters

hms_lincs_id (str) – The HMS LINCS ID of the small molecule.

Returns

The name of the small molecule.

Return type

str

get_small_molecule_refs(hms_lincs_id)

Get the id refs of a small molecule from the LINCS sm metadata.

Parameters

hms_lincs_id (str) – The HMS LINCS ID of the small molecule.

Returns

A dictionary of references.

Return type

dict

indra.databases.lincs_client.get_drug_target_data()

Load the csv into a list of dicts containing the LINCS drug target data.

Returns

data – A list of dicts, each keyed based on the header of the csv, with values as the corresponding column values.

Return type

list[dict]

indra.databases.lincs_client.load_lincs_csv(url)

Helper function to turn csv rows into dicts.

MeSH client (indra.databases.mesh_client)

indra.databases.mesh_client.get_db_mapping(mesh_id)

Return mapping to another name space for a MeSH ID, if it exists.

Parameters

mesh_id (str) – The MeSH ID whose mappings is to be returned.

Returns

A tuple consisting of a DB namespace and ID for the mapping or None if not available.

Return type

tuple or None

indra.databases.mesh_client.get_go_id(mesh_id)

Return a GO ID corresponding to the given MeSH ID.

Parameters

mesh_id (str) – MeSH ID to map to GO

Returns

The GO ID corresponding to the given MeSH ID, or None if not available.

Return type

str

indra.databases.mesh_client.get_mesh_id_from_db_id(db_ns, db_id)

Return a MeSH ID mapped from another namespace and ID.

Parameters

• db_ns (str) – A namespace corresponding to db_id.

• db_id (str) – An ID in the given namespace.

Returns

The MeSH ID corresponding to the given namespace and ID if available, otherwise None.

Return type

str or None

indra.databases.mesh_client.get_mesh_id_from_go_id(go_id)

Return a MeSH ID corresponding to the given GO ID.

Parameters

go_id (str) – GO ID to map to MeSH

Returns

The MeSH ID corresponding to the given GO ID, or None if not available.

Return type

str

indra.databases.mesh_client.get_mesh_id_name(mesh_term, offline=False)

Get the MESH ID and name for the given MESH term.

Uses the mappings table in indra/resources; if the MESH term is not listed there, falls back on the NLM REST API.

Parameters

• mesh_term (str) – MESH Descriptor or Concept name, e.g. ‘Breast Cancer’.

• offline (bool) – Whether to allow queries to the NLM REST API if the given MESH term is not contained in INDRA’s internal MESH mappings file. Default is False (allows REST API queries).

Returns

Returns a 2-tuple of the form (id, name) with the ID of the descriptor corresponding to the MESH label, and the descriptor name (which may not exactly match the name provided as an argument if it is a Concept name). If the query failed, or no descriptor corresponding to the name was found, returns a tuple of (None, None).

Return type

tuple of strs

indra.databases.mesh_client.get_mesh_id_name_from_web(mesh_term)

Get the MESH ID and name for the given MESH term using the NLM REST API.

Parameters

mesh_term (str) – MESH Descriptor or Concept name, e.g. ‘Breast Cancer’.

Returns

Returns a 2-tuple of the form (id, name) with the ID of the descriptor corresponding to the MESH label, and the descriptor name (which may not exactly match the name provided as an argument if it is a Concept name). If the query failed, or no descriptor corresponding to the name was found, returns a tuple of (None, None).

Return type

tuple of strs

indra.databases.mesh_client.get_mesh_name(mesh_id, offline=False)

Get the MESH label for the given MESH ID.

Uses the mappings table in indra/resources; if the MESH ID is not listed there, falls back on the NLM REST API.

Parameters

• mesh_id (str) – MESH Identifier, e.g. ‘D003094’.

• offline (bool) – Whether to allow queries to the NLM REST API if the given MESH ID is not contained in INDRA’s internal MESH mappings file. Default is False (allows REST API queries).

Returns

Label for the MESH ID, or None if the query failed or no label was found.

Return type

str

indra.databases.mesh_client.get_mesh_name_from_web(mesh_id)

Get the MESH label for the given MESH ID using the NLM REST API.

Parameters

mesh_id (str) – MESH Identifier, e.g. ‘D003094’.

Returns

Label for the MESH ID, or None if the query failed or no label was found.

Return type

str

indra.databases.mesh_client.get_mesh_tree_numbers(mesh_id)

Return MeSH tree IDs associated with a MeSH ID from the resource file.

This function can handle supplementary concepts by first mapping them to primary terms and then collecting all the tree numbers for the mapped primary terms.

Parameters

mesh_id (str) – The MeSH ID whose tree IDs should be returned.

Returns

A list of MeSH tree IDs.

Return type

list[str]

indra.databases.mesh_client.get_mesh_tree_numbers_from_web(mesh_id)

Return MeSH tree IDs associated with a MeSH ID from the web.

Parameters

mesh_id (str) – The MeSH ID whose tree IDs should be returned.

Returns

A list of MeSH tree IDs.

Return type

list[str]

indra.databases.mesh_client.get_primary_mappings(db_id)

Return the list of primary terms a supplementary term is mapped to.

See https://www.nlm.nih.gov/mesh/xml_data_elements.html#HeadingMappedTo.

Parameters

db_id (str) – A supplementary MeSH ID.

Return type

List[str]

Returns

The list of primary MeSH terms that the supplementary concept is heading-mapped to.

indra.databases.mesh_client.has_tree_prefix(mesh_id, tree_prefix)

Return True if the given MeSH ID has the given tree prefix.

indra.databases.mesh_client.is_disease(mesh_id)

Return True if the given MeSH ID is a disease.

indra.databases.mesh_client.is_enzyme(mesh_id)

Return True if the given MeSH ID is an enzyme.

indra.databases.mesh_client.is_molecular(mesh_id)

Return True if the given MeSH ID is a chemical or drug (incl protein).

indra.databases.mesh_client.is_protein(mesh_id)

Return True if the given MeSH ID is a protein.

GO client (indra.databases.go_client)

A client to the Gene Ontology.

indra.databases.go_client.get_go_id_from_label(label)

Get ID corresponding to a given GO label.

Parameters

label (str) – The GO label to get the ID for.

Returns

Identifier corresponding to the GO label, starts with GO:.

Return type

str

indra.databases.go_client.get_go_id_from_label_or_synonym(label)

Get ID corresponding to a given GO label or synonym

Parameters

label (str) – The GO label or synonym to get the ID for.

Returns

Identifier corresponding to the GO label or synonym, starts with GO:.

Return type

str

indra.databases.go_client.get_go_label(go_id)

Get label corresponding to a given GO identifier.

Parameters

go_id (str) – The GO identifier. Should include the GO: prefix, e.g., GO:1903793 (positive regulation of anion transport).

Returns

Label corresponding to the GO ID.

Return type

str

indra.databases.go_client.get_namespace(go_id)

Return the GO namespace associated with a GO ID.

Parameters

go_id (str) – The GO ID to get the namespace for

Return type

Optional[str]

Returns

The GO namespace for the given ID. This is one of molecular_function, biological_process or cellular_component. If the GO ID is not available as an entry, None is returned.

indra.databases.go_client.get_primary_id(go_id)

Get primary ID corresponding to an alternative/deprecated GO ID.

Parameters

go_id (str) – The GO ID to get the primary ID for.

Returns

Primary identifier corresponding to the given ID.

Return type

str

indra.databases.go_client.get_valid_location(loc)

Return a valid GO label based on an ID, label or synonym.

The rationale behind this function is that many sources produce cellular locations that are arbitrarily either GO IDs (sometimes without the prefix and sometimes outdated) or labels or synonyms. This function handles all these cases and returns a valid GO label in case one is available, otherwise None.

Parameters

loc (txt) – The location that needst o be canonicalized.

Returns

The valid location string is available, otherwise None.

Return type

str or None

PubChem client (indra.databases.pubchem_client)

indra.databases.pubchem_client.get_inchi_key(pubchem_cid)

Return the InChIKey for a given PubChem CID.

Parameters

pubchem_cid (str) – The PubChem CID whose InChIKey should be returned.

Returns

The InChIKey corresponding to the PubChem CID.

Return type

str

indra.databases.pubchem_client.get_json_record(pubchem_cid)

Return the JSON record of a given PubChem CID.

Parameters

pubchem_cid (str) – The PubChem CID whose record should be returned.

Returns

The record deserialized from JSON.

Return type

dict

indra.databases.pubchem_client.get_preferred_compound_ids(pubchem_cid)

Return a list of preferred CIDs for a given PubChem CID.

Parameters

pubchem_cid (str) – The PubChem CID whose preferred CIDs should be returned.

Returns

The list of preferred CIDs for the given CID. If there are no preferred CIDs for the given CID then an empty list is returned.

Return type

list of str

miRBase client (indra.databases.mirbase_client)

A client to miRBase.

indra.databases.mirbase_client.get_hgnc_id_from_mirbase_id(mirbase_id)

Return the HGNC ID corresponding to the given miRBase ID.

Parameters

mirbase_id (str) – The miRBase ID to be converted. Example: “MI0000060”

Returns

hgnc_id – The HGNC ID corresponding to the given miRBase ID.

Return type

str

indra.databases.mirbase_client.get_mirbase_id_from_hgnc_id(hgnc_id)

Return the HGNC ID corresponding to the given miRBase ID.

Parameters

hgnc_id (str) – An HGNC identifier to convert to miRBase, if it is indeed an miRNA. Example: “31476”

Returns

mirbase_id – The miRBase ID corresponding to the given HGNC ID.

Return type

str

indra.databases.mirbase_client.get_mirbase_id_from_hgnc_symbol(hgnc_symbol)

Return the HGNC gene symbol corresponding to the given miRBase ID.

Parameters

hgnc_symbol (str) – An HGNC gene symbol to convert to miRBase, if it is indeed an miRNA. Example: “MIR19B2”

Returns

mirbase_id – The miRBase ID corresponding to the given HGNC gene symbol.

Return type

str

indra.databases.mirbase_client.get_mirbase_id_from_mirbase_name(mirbase_name)

Return the miRBase identifier corresponding to the given miRBase name.

Parameters

mirbase_name (str) – The miRBase ID to be converted. Example: “hsa-mir-19b-2”

Returns

mirbase_id – The miRBase ID corresponding to the given miRBase name.

Return type

str

indra.databases.mirbase_client.get_mirbase_name_from_mirbase_id(mirbase_id)

Return the miRBase name corresponding to the given miRBase ID.

Parameters

mirbase_id (str) – The miRBase ID to be converted. Example: “MI0000060”

Returns

mirbase_name – The miRBase name corresponding to the given miRBase ID.

Return type

str

Experimental Factor Ontology (EFO) client (indra.databases.efo_client)

A client to EFO.

indra.databases.efo_client.get_efo_id_from_efo_name(efo_name)

Return the EFO identifier corresponding to the given EFO name.

Parameters

efo_name (str) – The EFO name to be converted. Example: “gum cancer”

Returns

efo_id – The EFO identifier corresponding to the given EFO name.

Return type

str

indra.databases.efo_client.get_efo_name_from_efo_id(efo_id)

Return the EFO name corresponding to the given EFO ID.

Parameters

efo_id (str) – The EFO identifier to be converted. Example: “0005557”

Returns

efo_name – The EFO name corresponding to the given EFO identifier.

Return type

str

Human Phenotype Ontology (HP) client (indra.databases.hp_client)

A client to HP.

indra.databases.hp_client.get_hp_id_from_hp_name(hp_name)

Return the HP identifier corresponding to the given HP name.

Parameters

hp_name (str) – The HP name to be converted. Example: “Nocturia”

Returns

hp_id – The HP identifier corresponding to the given HP name.

Return type

str

indra.databases.hp_client.get_hp_name_from_hp_id(hp_id)

Return the HP name corresponding to the given HP ID.

Parameters

hp_id (str) – The HP identifier to be converted. Example: “HP:0000017”

Returns

hp_name – The HP name corresponding to the given HP identifier.

Return type

str

Disease Ontology (DOID) client (indra.databases.doid_client)

A client to the Disease Ontology.

indra.databases.doid_client.get_doid_id_from_doid_alt_id(doid_alt_id)

Return the identifier corresponding to the given Disease Ontology alt id.

Parameters

doid_alt_id (str) – The Disease Ontology alt id to be converted. Example: “DOID:267”

Returns

doid_id – The Disease Ontology identifier corresponding to the given alt id.

Return type

str

indra.databases.doid_client.get_doid_id_from_doid_name(doid_name)

Return the identifier corresponding to the given Disease Ontology name.

Parameters

doid_name (str) – The Disease Ontology name to be converted. Example: “Nocturia”

Returns

doid_id – The Disease Ontology identifier corresponding to the given name.

Return type

str

indra.databases.doid_client.get_doid_name_from_doid_id(doid_id)

Return the name corresponding to the given Disease Ontology ID.

Parameters

doid_id (str) – The Disease Ontology identifier to be converted. Example: “DOID:0000017”

Returns

doid_name – The DOID name corresponding to the given DOID identifier.

Return type

str

Infectious Disease Ontology client (indra.databases.ido_client)

A client to OWL.

indra.databases.ido_client.get_ido_id_from_ido_name(ido_name)

Return the HP identifier corresponding to the given IDO name.

Parameters

ido_name (str) – The IDO name to be converted. Example: “parasite role”

Return type

Optional[str]

Returns

The IDO identifier corresponding to the given IDO name.

indra.databases.ido_client.get_ido_name_from_ido_id(ido_id)

Return the HP name corresponding to the given HP ID.

Parameters

ido_id (str) – The IDO identifier to be converted. Example: “0000403”

Return type

Optional[str]

Returns

The IDO name corresponding to the given IDO identifier.

Taxonomy client (indra.databases.taxonomy_client)

Client to access the Entrez Taxonomy web service.

indra.databases.taxonomy_client.get_taxonomy_id(name)

Return the taxonomy ID corresponding to a taxonomy name.

Parameters

name (str) – The name of the taxonomy entry. Example: “Severe acute respiratory syndrome coronavirus 2”

Returns

The taxonomy ID corresponding to the given name or None if not available.

Return type

str or None

DrugBank client (indra.databases.drugbank_client)

Client for interacting with DrugBank entries.

indra.databases.drugbank_client.get_chebi_id(drugbank_id)

Return a mapping for a DrugBank ID to CHEBI.

Parameters

drugbank_id (str) – DrugBank ID to map.

Returns

The ID mapped to CHEBI or None if not available.

Return type

str or None

indra.databases.drugbank_client.get_chembl_id(drugbank_id)

Return a mapping for a DrugBank ID to CHEMBL.

Parameters

drugbank_id (str) – DrugBank ID to map.

Returns

The ID mapped to CHEMBL or None if not available.

Return type

str or None

indra.databases.drugbank_client.get_db_mapping(drugbank_id, db_ns)

Return a mapping for a DrugBank ID to a given name space.

Parameters

• drugbank_id (str) – DrugBank ID to map.

• db_ns (str) – The database name space to map to.

Returns

The ID mapped to the given name space or None if not available.

Return type

str or None

indra.databases.drugbank_client.get_drugbank_id_from_chebi_id(chebi_id)

Return DrugBank ID from a CHEBI ID.

Parameters

chebi_id (str) – CHEBI ID to map.

Returns

The mapped DrugBank ID or None if not available.

Return type

str or None

indra.databases.drugbank_client.get_drugbank_id_from_chembl_id(chembl_id)

Return DrugBank ID from a CHEMBL ID.

Parameters

chembl_id (str) – CHEMBL ID to map.

Returns

The mapped DrugBank ID or None if not available.

Return type

str or None

indra.databases.drugbank_client.get_drugbank_id_from_db_id(db_ns, db_id)

Return DrugBank ID from a database name space and ID.

Parameters

• db_ns (str) – Database name space.

• db_id (str) – Database ID.

Returns

The mapped DrugBank ID or None if not available.

Return type

str or None

indra.databases.drugbank_client.get_drugbank_name(drugbank_id)

Return the DrugBank standard name for a given DrugBank ID.

Parameters

drugbank_id (str) – DrugBank ID to get the name for

Returns

The name corresponding to the given DrugBank ID or None if not available.

Return type

str or None

OBO client (indra.databases.obo_client)

A client for OBO-sourced identifier mappings.

class indra.databases.obo_client.OboClient(prefix)

A base client for data that’s been grabbed via OBO

static entries_from_graph(obo_graph, prefix, remove_prefix=False, allowed_synonyms=None, allowed_external_ns=None)

Return processed entries from an OBO graph.

classmethod update_resource(directory, url, prefix, *args, remove_prefix=False, allowed_synonyms=None, allowed_external_ns=None, force=False)

Write the OBO information to files in the given directory.

class indra.databases.obo_client.OntologyClient(prefix)

A base client class for OBO and OWL ontologies.

get_id_from_alt_id(db_alt_id)

Return the canonical database id corresponding to the alt id.

Parameters

db_alt_id (str) – The alt id to be converted.

Return type

Optional[str]

Returns

The ID corresponding to the given alt id.

get_id_from_name(db_name)

Return the database identifier corresponding to the given name.

Parameters

db_name (str) – The name to be converted.

Return type

Optional[str]

Returns

The ID corresponding to the given name.

get_id_from_name_or_synonym(txt)

Return the database id corresponding to the given name or synonym.

Note that the way the OboClient is constructed, ambiguous synonyms are filtered out. Further, this function prioritizes names over synonyms (i.e., it first looks up the ID by name, and only if that fails, it attempts a synonym-based lookup). Overall, these mappings are guaranteed to be many-to-one.

Parameters

txt (str) – The name or synonym to be converted.

Return type

Optional[str]

Returns

The ID corresponding to the given name or synonym.

get_name_from_id(db_id)

Return the database name corresponding to the given database ID.

Parameters

db_id (str) – The ID to be converted.

Return type

Optional[str]

Returns

The name corresponding to the given ID.

get_relation(db_id, rel_type)

Return the isa relationships corresponding to a given ID.

Parameters

• db_id (str) – The ID whose isa relationships should be returned

• rel_type (str) – The type of relationships to get, e.g., is_a, part_of

Return type

List[str]

Returns

The IDs of the terms that are in the given relation with the given ID.

get_relations(db_id)

Return the isa relationships corresponding to a given ID.

Parameters

db_id (str) – The ID whose isa relationships should be returned

Return type

Mapping[str, List[str]]

Returns

A dict keyed by relation type with each entry a list of IDs of the terms that are in the given relation with the given ID.

OWL client (indra.databases.owl_client)

A client for OWL-sourced identifier mappings.

class indra.databases.owl_client.OwlClient(prefix)

A base client for data that’s been grabbed via OWL.

static entry_from_term(term, prefix, remove_prefix=False, allowed_external_ns=None)

Create a data dictionary from a Pronto term.

Return type

Mapping[str, Any]