RLIMS-P (indra.sources.rlimsp)

RLIMS-P is a rule-based reading system which extracts phosphorylation relationships with sites from text. RLIMS-P exposes a web service to submit PubMed IDs and PMC IDs for processing.

See also: https://research.bioinformatics.udel.edu/rlimsp/ and https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4568560/

RLIMS-P API (indra.sources.rlimsp.api)

indra.sources.rlimsp.api.process_from_json_file(filename, doc_id_type=None)[source]

DEPRECATED: use process_jsonl_file instead.

indra.sources.rlimsp.api.process_from_jsonish_str(jsonish_str, doc_id_type=None)[source]

DEPRECATED: use process_jsonl_str instead.

indra.sources.rlimsp.api.process_from_webservice(id_val, id_type='pmcid', source='pmc')[source]

Return an output from RLIMS-p for the given PubMed ID or PMC ID.

The web service is documented at: https://research.bioinformatics.udel.edu/itextmine/api/. The /data/rlims URL endpoint is extended with three additional elements: /{collection}/{key}/{value} where collection is “medline” or “pmc”, key is “pmid” or “pmcid”, and value is a specific PMID or PMCID.

Parameters

  • id_val (str) – A PMCID, with the prefix PMC, or PMID, with no prefix, of the paper to be “read”. Corresponds to the “value” argument of the REST API.

  • id_type (Optional[str]) – Either ‘pmid’ or ‘pmcid’. The default is ‘pmcid’. Corresponds to the “key” argument of the REST API.

  • source (Optional[str]) – Either ‘pmc’ or ‘medline’, whether you want pmc fulltext or medline abstracts. Corresponds to the “collection” argument of the REST API.

Returns

An RlimspProcessor which contains a list of extracted INDRA Statements in its statements attribute.

Return type

indra.sources.rlimsp.processor.RlimspProcessor

indra.sources.rlimsp.api.process_jsonl_file(filename, doc_id_type=None)[source]

Process RLIMSP extractions from a bulk-download JSON-L file.

Parameters

  • filename (str) – Path to the JSON file.

  • doc_id_type (Optional[str]) – In some cases the RLIMS-P paragraph info doesn’t contain ‘pmid’ or ‘pmcid’ explicitly, instead if contains a ‘docId’ key. This parameter allows defining what ID type ‘docId’ sould be interpreted as. Its values should be ‘pmid’ or ‘pmcid’ or None if not used.

Returns

An RlimspProcessor which contains a list of extracted INDRA Statements in its statements attribute.

Return type

indra.sources.rlimsp.processor.RlimspProcessor

indra.sources.rlimsp.api.process_jsonl_str(jsonl_str, doc_id_type=None)[source]

Process RLIMSP extractions from a JSON-L string.

Parameters

  • jsonl_str (str) – The contents of one of the JSON-L files you can find here: https://hershey.dbi.udel.edu/textmining/export

  • doc_id_type (Optional[str]) – In some cases the RLIMS-P paragraph info doesn’t contain ‘pmid’ or ‘pmcid’ explicitly, instead if contains a ‘docId’ key. This parameter allows defining what ID type ‘docId’ sould be interpreted as. Its values should be ‘pmid’ or ‘pmcid’ or None if not used.

Returns

An RlimspProcessor which contains a list of extracted INDRA Statements in its statements attribute.

Return type

indra.sources.rlimsp.processor.RlimspProcessor

RLIMSP-P Processor (indra.sources.rlimsp.processor)

class indra.sources.rlimsp.processor.RlimspParagraph(p_info, doc_id_type)[source]

An object that represents a single RLIMS-P Paragraph.

class indra.sources.rlimsp.processor.RlimspProcessor(rlimsp_json, doc_id_type=None)[source]

Convert RLIMS-P JSON into INDRA Statements.

extract_statements()[source]

Extract the statements from the json.

indra.sources.rlimsp.processor.get_agent_from_entity_info(entity_info)[source]

Return an INDRA Agent by processing an entity_info dict.