hazyresearch/dd-genomics issues and pull requests

#100 - GV: Handle issue where e.g. "g." and "XXX" are split...

Issue - State: closed - Opened by ajratner over 9 years ago
Labels: bug, Candidate extraction

#100 - GV: Handle issue where e.g. "g." and "XXX" are split...

Issue - State: closed - Opened by ajratner over 9 years ago
Labels: bug, Candidate extraction

#99 - GV: Proper GV extractor (e.g. using learning / inference)

Issue - State: closed - Opened by ajratner over 9 years ago
Labels: Distant supervision, Feature, Candidate extraction

#99 - GV: Proper GV extractor (e.g. using learning / inference)

Issue - State: closed - Opened by ajratner over 9 years ago
Labels: Distant supervision, Feature, Candidate extraction

#98 - Run PubMed through parser

Issue - State: closed - Opened by ajratner over 9 years ago - 4 comments
Labels: Preprocessing, Data source, PRIORITY

#98 - Run PubMed through parser

Issue - State: closed - Opened by ajratner over 9 years ago - 4 comments
Labels: Preprocessing, Data source, PRIORITY

#97 - [bazaar] Add some methods in to handle random segments failing

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: bug, Preprocessing

#97 - [bazaar] Add some methods in to handle random segments failing

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: bug, Preprocessing

#96 - Document full pre-processing pipeline in main README.md

Issue - State: closed - Opened by ajratner over 9 years ago
Labels: Preprocessing

#96 - Document full pre-processing pipeline in main README.md

Issue - State: closed - Opened by ajratner over 9 years ago
Labels: Preprocessing

#95 - [bazaar] Fix distribute code to run all without failing -> RUN PMC through parser!

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: bug, Preprocessing, PRIORITY

#95 - [bazaar] Fix distribute code to run all without failing -> RUN PMC through parser!

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: bug, Preprocessing, PRIORITY

#94 - Get processing of docs running on AWS via bazaar/distribute

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: Preprocessing, PRIORITY

#94 - Get processing of docs running on AWS via bazaar/distribute

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: Preprocessing, PRIORITY

#93 - Create separate table with ref-doc-ids?

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: Preprocessing, Low priority

#93 - Create separate table with ref-doc-ids?

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: Preprocessing, Low priority

#92 - Abbreviation detection for phenotypes

Issue - State: closed - Opened by Colossus over 9 years ago - 1 comment
Labels: Distant supervision, Feature, Candidate extraction, PRIORITY

#92 - Abbreviation detection for phenotypes

Issue - State: closed - Opened by Colossus over 9 years ago - 1 comment
Labels: Distant supervision, Feature, Candidate extraction, PRIORITY

#91 - PNAS not in PMC? Missing any others?

Issue - State: closed - Opened by ajratner over 9 years ago - 11 comments
Labels: Data source

#91 - PNAS not in PMC? Missing any others?

Issue - State: closed - Opened by ajratner over 9 years ago - 11 comments
Labels: Data source

#90 - GV, GV-P: integration with API

Issue - State: open - Opened by ajratner over 9 years ago - 1 comment
Labels: Dashboard / etc, PRIORITY

#90 - GV, GV-P: integration with API

Issue - State: open - Opened by ajratner over 9 years ago - 1 comment
Labels: Dashboard / etc, PRIORITY

#89 - GV-P: Re-purpose G-P code to handle this (w/ ClinVar DS data)

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: Distant supervision, Candidate extraction, PRIORITY

#89 - GV-P: Re-purpose G-P code to handle this (w/ ClinVar DS data)

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: Distant supervision, Candidate extraction, PRIORITY

#88 - GV-P: Join ClinVar + OMIM to get DS set for GV-P relations

Issue - State: closed - Opened by ajratner over 9 years ago
Labels: Distant supervision, Data source, PRIORITY

#88 - GV-P: Join ClinVar + OMIM to get DS set for GV-P relations

Issue - State: closed - Opened by ajratner over 9 years ago
Labels: Distant supervision, Data source, PRIORITY

#87 - GV: Add in simple regex tagger

Issue - State: closed - Opened by ajratner over 9 years ago
Labels: Candidate extraction, PRIORITY

#87 - GV: Add in simple regex tagger

Issue - State: closed - Opened by ajratner over 9 years ago
Labels: Candidate extraction, PRIORITY

#86 - Parser fix

Pull Request - State: closed - Opened by ajratner over 9 years ago

#86 - Parser fix

Pull Request - State: closed - Opened by ajratner over 9 years ago

#85 - Move coreNLP wrapper from bazaar -> dd-genomics/parser code

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: Preprocessing, Low priority

#85 - Move coreNLP wrapper from bazaar -> dd-genomics/parser code

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: Preprocessing, Low priority

#84 - REDO SCHEMA: separate doc_id, section_id, sent_id, ref_doc_id

Issue - State: closed - Opened by ajratner over 9 years ago - 5 comments
Labels: Preprocessing

#84 - REDO SCHEMA: separate doc_id, section_id, sent_id, ref_doc_id

Issue - State: closed - Opened by ajratner over 9 years ago - 5 comments
Labels: Preprocessing

#83 - Is PLoS (+ BMC) a subset of PMC-OA?

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: Data source

#83 - Is PLoS (+ BMC) a subset of PMC-OA?

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: Data source

#82 - Output refs as ".Ref" & with correct doc_id (i.e. their own, not the article containing them...)

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: bug, Preprocessing

#82 - Output refs as ".Ref" & with correct doc_id (i.e. their own, not the article containing them...)

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: bug, Preprocessing

#81 - Clean up parser run script- load metadata file in to db, etc.

Issue - State: closed - Opened by ajratner over 9 years ago
Labels: Preprocessing

#81 - Clean up parser run script- load metadata file in to db, etc.

Issue - State: closed - Opened by ajratner over 9 years ago
Labels: Preprocessing

#80 - [bazaar] Modify parser code so that arbitrary json fields of input are passed -> sentences

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: Preprocessing

#80 - [bazaar] Modify parser code so that arbitrary json fields of input are passed -> sentences

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: Preprocessing

#79 - Set up and document AWS pipeline for pre-processing

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: Preprocessing, PRIORITY

#79 - Set up and document AWS pipeline for pre-processing

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: Preprocessing, PRIORITY

#78 - Modify XML parser code so as to pick up years for titles

Issue - State: closed - Opened by ajratner over 9 years ago - 2 comments
Labels: Preprocessing

#78 - Modify XML parser code so as to pick up years for titles

Issue - State: closed - Opened by ajratner over 9 years ago - 2 comments
Labels: Preprocessing

#77 - Manually add a handful of articles that solve patients we have already solved

Issue - State: closed - Opened by gbgbg over 9 years ago - 10 comments

#77 - Manually add a handful of articles that solve patients we have already solved

Issue - State: closed - Opened by gbgbg over 9 years ago - 10 comments

#76 - Adapt Parser/Schema to PubMed

Issue - State: closed - Opened by Colossus over 9 years ago - 9 comments

#76 - Adapt Parser/Schema to PubMed

Issue - State: closed - Opened by Colossus over 9 years ago - 9 comments

#75 - "Falls" is a phenotype

Issue - State: closed - Opened by Colossus over 9 years ago - 1 comment
Labels: bug, Candidate extraction

#75 - "Falls" is a phenotype

Issue - State: closed - Opened by Colossus over 9 years ago - 1 comment
Labels: bug, Candidate extraction

#74 - Store logs from API

Issue - State: open - Opened by ajratner over 9 years ago - 1 comment
Labels: PRIORITY

#74 - Store logs from API

Issue - State: open - Opened by ajratner over 9 years ago - 1 comment
Labels: PRIORITY

#73 - gene_entity should always reference the canonical gene name or ensembl ID

Issue - State: closed - Opened by Colossus over 9 years ago - 1 comment

#73 - gene_entity should always reference the canonical gene name or ensembl ID

Issue - State: closed - Opened by Colossus over 9 years ago - 1 comment

#72 - Allow cross-origin API requests

Issue - State: closed - Opened by ajratner over 9 years ago - 3 comments
Labels: bug, PRIORITY

#72 - Allow cross-origin API requests

Issue - State: closed - Opened by ajratner over 9 years ago - 3 comments
Labels: bug, PRIORITY

#71 - Custom Dashboard Report with Gill's questions

Issue - State: closed - Opened by Colossus over 9 years ago - 1 comment
Labels: Dashboard / etc

#71 - Custom Dashboard Report with Gill's questions

Issue - State: closed - Opened by Colossus over 9 years ago - 1 comment
Labels: Dashboard / etc

#70 - Extractor for disease inheritance modes

Issue - State: closed - Opened by Colossus over 9 years ago - 4 comments

#70 - Extractor for disease inheritance modes

Issue - State: closed - Opened by Colossus over 9 years ago - 4 comments

#69 - Separate Title, Abstract and Body text extraction

Issue - State: closed - Opened by Colossus over 9 years ago
Labels: Distant supervision, Candidate extraction

#69 - Separate Title, Abstract and Body text extraction

Issue - State: closed - Opened by Colossus over 9 years ago
Labels: Distant supervision, Candidate extraction

#68 - Debug titles only extraction

Issue - State: closed - Opened by Colossus over 9 years ago - 6 comments
Labels: bug, Distant supervision

#68 - Debug titles only extraction

Issue - State: closed - Opened by Colossus over 9 years ago - 6 comments
Labels: bug, Distant supervision

#67 - Count distinct gene_entity, pheno_entity and genepheno_entity for validation check after running on various datasets

Issue - State: closed - Opened by Colossus over 9 years ago - 1 comment
Labels: Dashboard / etc

#67 - Count distinct gene_entity, pheno_entity and genepheno_entity for validation check after running on various datasets

Issue - State: closed - Opened by Colossus over 9 years ago - 1 comment
Labels: Dashboard / etc

GitHub / hazyresearch/dd-genomics issues and pull requests