REACH (indra.sources.reach
)¶
REACH API (indra.sources.reach.reach_api
)¶
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indra.sources.reach.reach_api.
process_json_file
(file_name, citation=None)[source]¶ Return a ReachProcessor by processing the given REACH json file.
The output from the REACH parser is in this json format. This function is useful if the output is saved as a file and needs to be processed. For more information on the format, see: https://github.com/clulab/reach
Parameters: - file_name (str) – The name of the json file to be processed.
- citation (Optional[str]) – A PubMed ID passed to be used in the evidence for the extracted INDRA Statements. Default: None
Returns: rp – A ReachProcessor containing the extracted INDRA Statements in rp.statements.
Return type:
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indra.sources.reach.reach_api.
process_json_str
(json_str, citation=None)[source]¶ Return a ReachProcessor by processing the given REACH json string.
The output from the REACH parser is in this json format. For more information on the format, see: https://github.com/clulab/reach
Parameters: - json_str (str) – The json string to be processed.
- citation (Optional[str]) – A PubMed ID passed to be used in the evidence for the extracted INDRA Statements. Default: None
Returns: rp – A ReachProcessor containing the extracted INDRA Statements in rp.statements.
Return type:
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indra.sources.reach.reach_api.
process_nxml_file
(file_name, citation=None, offline=False)[source]¶ Return a ReachProcessor by processing the given NXML file.
NXML is the format used by PubmedCentral for papers in the open access subset.
Parameters: - file_name (str) – The name of the NXML file to be processed.
- citation (Optional[str]) – A PubMed ID passed to be used in the evidence for the extracted INDRA Statements. Default: None
- offline (Optional[bool]) – If set to True, the REACH system is ran offline. Otherwise (by default) the web service is called. Default: False
Returns: rp – A ReachProcessor containing the extracted INDRA Statements in rp.statements.
Return type:
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indra.sources.reach.reach_api.
process_nxml_str
(nxml_str, citation=None, offline=False)[source]¶ Return a ReachProcessor by processing the given NXML string.
NXML is the format used by PubmedCentral for papers in the open access subset.
Parameters: - nxml_str (str) – The NXML string to be processed.
- citation (Optional[str]) – A PubMed ID passed to be used in the evidence for the extracted INDRA Statements. Default: None
- offline (Optional[bool]) – If set to True, the REACH system is ran offline. Otherwise (by default) the web service is called. Default: False
Returns: rp – A ReachProcessor containing the extracted INDRA Statements in rp.statements.
Return type:
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indra.sources.reach.reach_api.
process_pmc
(pmc_id, offline=False)[source]¶ Return a ReachProcessor by processing a paper with a given PMC id.
Uses the PMC client to obtain the full text. If it’s not available, None is returned.
Parameters: - pmc_id (str) – The ID of a PubmedCentral article. The string may start with PMC but passing just the ID also works. Examples: 3717945, PMC3717945 https://www.ncbi.nlm.nih.gov/pmc/
- offline (Optional[bool]) – If set to True, the REACH system is ran offline. Otherwise (by default) the web service is called. Default: False
Returns: rp – A ReachProcessor containing the extracted INDRA Statements in rp.statements.
Return type:
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indra.sources.reach.reach_api.
process_pubmed_abstract
(pubmed_id, offline=False)[source]¶ Return a ReachProcessor by processing an abstract with a given Pubmed id.
Uses the Pubmed client to get the abstract. If that fails, None is returned.
Parameters: - pubmed_id (str) – The ID of a Pubmed article. The string may start with PMID but passing just the ID also works. Examples: 27168024, PMID27168024 https://www.ncbi.nlm.nih.gov/pubmed/
- offline (Optional[bool]) – If set to True, the REACH system is ran offline. Otherwise (by default) the web service is called. Default: False
Returns: rp – A ReachProcessor containing the extracted INDRA Statements in rp.statements.
Return type:
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indra.sources.reach.reach_api.
process_text
(text, citation=None, offline=False)[source]¶ Return a ReachProcessor by processing the given text.
Parameters: - text (str) – The text to be processed.
- citation (Optional[str]) – A PubMed ID passed to be used in the evidence for the extracted INDRA Statements. This is used when the text to be processed comes from a publication that is not otherwise identified. Default: None
- offline (Optional[bool]) – If set to True, the REACH system is ran offline. Otherwise (by default) the web service is called. Default: False
Returns: rp – A ReachProcessor containing the extracted INDRA Statements in rp.statements.
Return type:
REACH Processor (indra.sources.reach.processor
)¶
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class
indra.sources.reach.processor.
ReachProcessor
(json_dict, pmid=None)[source]¶ The ReachProcessor extracts INDRA Statements from REACH parser output.
Parameters: - json_dict (dict) – A JSON dictionary containing the REACH extractions.
- pmid (Optional[str]) – The PubMed ID associated with the extractions. This can be passed in case the PMID cannot be determined from the extractions alone.`
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tree
¶ objectpath.Tree – The objectpath Tree object representing the extractions.
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statements
¶ list[indra.statements.Statement] – A list of INDRA Statements that were extracted by the processor.
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citation
¶ str – The PubMed ID associated with the extractions.
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all_events
¶ dict[str, str] – The frame IDs of all events by type in the REACH extraction.
REACH reader (indra.sources.reach.reach_reader
)¶
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class
indra.sources.reach.reach_reader.
ReachReader
[source]¶ The ReachReader wraps a singleton instance of the REACH reader.
This allows calling the reader many times without having to wait for it to start up each time.
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api_ruler
¶ org.clulab.reach.apis.ApiRuler – An instance of the REACH ApiRuler class (java object).
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