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Add curation sheet with 500 BEL statements
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@ddomingof there's definitely room for more. Also, looks like there are quite a few miRNAs that get missed by INDRA. See sorgerlab/indra#255 at sorgerlab/indra#255
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@cthoyt
cthoyt committed Feb 15, 2019
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13 changes: 1 addition & 12 deletions curation/README.rst
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Curation
========
1. Generate a PubMed identifier list:

.. code-block:: sh
$ cat pubmeds.tsv | cut -f 1 | grep -e "^\d\+$" > pubmeds.txt
2. Generate curation sheet and pickles:

.. code-block:: sh
$ bel-enrichment from-pmids --pmids pubmeds.txt --output curation.tsv --pickle-file statements.pkl
The ``generate.sh`` script was used to create ``pmids.txt``, ``statements.pkl``, and ``curation.tsv``. It is logged with ``generation-log.txt``.
502 changes: 502 additions & 0 deletions curation/curation.tsv
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7 changes: 7 additions & 0 deletions curation/generate.sh
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#!/usr/bin/env bash

# Slice out just the identifiers column and skip the missing entries
cat pubmeds.tsv | cut -f 1 | grep -e "^\d\+$" > pubmeds.txt

# Generate INDRA statements and BEL from those PubMed identifiers
bel-enrichment from_pmids --pmids pubmeds.txt --output curation.tsv --pickle-file statements.pkl 2> generation-log.txt
71 changes: 71 additions & 0 deletions curation/generation-log.txt
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WARNING: [2019-02-15 15:54:58] indra.sources.reach.api - Could not import jnius, offline reading option will not be available.
WARNING: [2019-02-15 15:54:58] indra.config - Key SITEMAPPER_CACHE_PATH not in environment or config file.
INFO: [2019-02-15 15:54:58] indra.sources.indra_db_rest.util - url and query string: https://db.indra.bio/statements/from_papers
INFO: [2019-02-15 15:54:58] indra.sources.indra_db_rest.util - headers: {'content-type': 'application/json'}
INFO: [2019-02-15 15:54:58] indra.sources.indra_db_rest.util - data: {'ids': [{'id': '19969070', 'type': 'pmid'}, {'id': '21387008', 'type': 'pmid'}, {'id': '25036103', 'type': 'pmid'}, {'id': '30063760', 'type': 'pmid'}, {'id': '21035514', 'type': 'pmid'}, {'id': '28116245', 'type': 'pmid'}, {'id': '28124620', 'type': 'pmid'}, {'id': '29417334', 'type': 'pmid'}, {'id': '26205378', 'type': 'pmid'}, {'id': '25407931', 'type': 'pmid'}, {'id': '24559646', 'type': 'pmid'}, {'id': '25534921', 'type': 'pmid'}]}
INFO: [2019-02-15 15:54:58] indra.sources.indra_db_rest.util - params: {'ev_limit': 10, 'best_first': True, 'max_stmts': None, 'api_key': '[api-key]'}
INFO: [2019-02-15 15:54:59] indra.tools.assemble_corpus - Combining duplicates on 161 statements...
INFO: [2019-02-15 15:54:59] indra.tools.assemble_corpus - 161 unique statements
INFO: [2019-02-15 15:54:59] indra.tools.assemble_corpus - Combining related on 161 statements...
INFO: [2019-02-15 15:55:00] indra.preassembler - Grouping Activation (89)
INFO: [2019-02-15 15:55:03] indra.preassembler - Grouping Complex (5)
INFO: [2019-02-15 15:55:03] indra.preassembler - Grouping DecreaseAmount (1)
INFO: [2019-02-15 15:55:03] indra.preassembler - Grouping IncreaseAmount (6)
INFO: [2019-02-15 15:55:03] indra.preassembler - Grouping Inhibition (43)
INFO: [2019-02-15 15:55:03] indra.preassembler - Grouping Phosphorylation (17)
INFO: [2019-02-15 15:55:03] indra.tools.assemble_corpus - Filtering 161 statements for top-level...
INFO: [2019-02-15 15:55:03] indra.tools.assemble_corpus - 154 statements after filter...
INFO: [2019-02-15 15:55:03] indra.tools.assemble_corpus - 154 top-level statements
INFO: [2019-02-15 15:55:03] indra.tools.assemble_corpus - Filtering 154 statements to above 0.300000 belief
INFO: [2019-02-15 15:55:03] indra.tools.assemble_corpus - 154 statements after filter...
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent 7KCHO() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent Insulin/IGF-1/PI3K() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent Phosphoinositides 3-kinases() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent RSK1/2 activator() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent RSK1/2() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent RSKs() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent RSKs() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent ST2825 inhibitor() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent ST2825 inhibitor() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent TBK1 inhibitor() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent TLR4 receptor() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent beta-interferon(activity) has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent beta-interferon(activity) has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent ikappaB() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent miR-126() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent miR-126() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent Abeta 1-42 toxicity(activity) has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent miR-126() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent Abeta 1-42(activity) has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent miR-126() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent miR-126() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent GSK-3beta ratios(activity) has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent miR-126() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent miR-126() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent IGF-1/PI3K/AKT(activity) has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent miR-126() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent miR-126() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent Tg6799 mutant(activity) has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent IGF-1 receptor() has no grounding.
INFO: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Skipping modification of type modification on agent VC(mods: (modification))
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent alpha-syn() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent double-stranded RNA-activated protein kinase(activity) has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent beta-interferon(activity) has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent Necrostatin() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent SL0101() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent SL0101() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent SOCS1-3() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent YVAD-CMK() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent miR-126() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent miR-126() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent miR-126() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent miR-126() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent miR-126() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent miR-433() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent miR-433() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent miR-98() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent miR-98() has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent ikappaB(mods: (phosphorylation)) has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent ikappaB(mods: (phosphorylation)) has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent miR-98(mods: (modification)) has no grounding.
WARNING: [2019-02-15 15:55:03] indra.assemblers.pybel.assembler - Agent miR-98(mods: (modification)) has no grounding.
3 changes: 0 additions & 3 deletions curation/pubmeds.txt
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PubMedID
19969070
21387008
25036103
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25407931
24559646
25534921
X
X
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