hazyresearch/dd-genomics issues and pull requests

#50 - Extract relationships from abstracts and titles only

Issue - State: closed - Opened by Colossus over 9 years ago - 3 comments

#50 - Extract relationships from abstracts and titles only

Issue - State: closed - Opened by Colossus over 9 years ago - 3 comments

#49 - Make dashboard have 'multinomial' values

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

#49 - Make dashboard have 'multinomial' values

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

#48 - Association VS. Causation supervision rules

Issue - State: closed - Opened by Colossus over 9 years ago - 3 comments
Labels: Distant supervision, PRIORITY

#48 - Association VS. Causation supervision rules

Issue - State: closed - Opened by Colossus over 9 years ago - 3 comments
Labels: Distant supervision, PRIORITY

#47 - Get Aaron, Gill, Johannes, (Alex?) to label set independently

Issue - State: closed - Opened by ajratner over 9 years ago - 12 comments
Labels: Data source, PRIORITY

#47 - Get Aaron, Gill, Johannes, (Alex?) to label set independently

Issue - State: closed - Opened by ajratner over 9 years ago - 12 comments
Labels: Data source, PRIORITY

#46 - Load PMID to HPO via mesh into database table + add PMID column to sentences_input

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

#46 - Load PMID to HPO via mesh into database table + add PMID column to sentences_input

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

#45 - Remove sentences from current sentences_input that do not contain a gene name

Issue - State: closed - Opened by Colossus over 9 years ago - 2 comments
Labels: Preprocessing, Data source

#45 - Remove sentences from current sentences_input that do not contain a gene name

Issue - State: closed - Opened by Colossus over 9 years ago - 2 comments
Labels: Preprocessing, Data source

#44 - Make pheno_extract_candidates less top-heavy!

Issue - State: closed - Opened by ajratner over 9 years ago - 3 comments
Labels: bug, Candidate extraction, Low priority

#44 - Make pheno_extract_candidates less top-heavy!

Issue - State: closed - Opened by ajratner over 9 years ago - 3 comments
Labels: bug, Candidate extraction, Low priority

#43 - GP: Add Multinomial {causation, association, NONE}

Issue - State: closed - Opened by ajratner over 9 years ago - 12 comments

#43 - GP: Add Multinomial {causation, association, NONE}

Issue - State: closed - Opened by ajratner over 9 years ago - 12 comments

#42 - Some sort of memory error w pheno_extract_candidates

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

#42 - Some sort of memory error w pheno_extract_candidates

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

#41 - Include noncanonical gene names in gene-pheno relationship extractor

Issue - State: closed - Opened by Colossus over 9 years ago - 2 comments

#41 - Include noncanonical gene names in gene-pheno relationship extractor

Issue - State: closed - Opened by Colossus over 9 years ago - 2 comments

#40 - Centralize HPO canonicalization / other HPO DAG functions in util

Issue - State: closed - Opened by ajratner over 9 years ago
Labels: Low priority, Data source

#40 - Centralize HPO canonicalization / other HPO DAG functions in util

Issue - State: closed - Opened by ajratner over 9 years ago
Labels: Low priority, Data source

#39 - Use Trends in Dashboard

Issue - State: closed - Opened by ajratner over 9 years ago
Labels: Dashboard / etc

#39 - Use Trends in Dashboard

Issue - State: closed - Opened by ajratner over 9 years ago
Labels: Dashboard / etc

#38 - List of common bio abbreviations

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

#38 - List of common bio abbreviations

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

#37 - Fix the genes canonical/noncanonical issue

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

#37 - Fix the genes canonical/noncanonical issue

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

#36 - Implement DS rule testing framework

Issue - State: closed - Opened by Colossus over 9 years ago
Labels: Distant supervision, Low priority, Dashboard / etc

#36 - Implement DS rule testing framework

Issue - State: closed - Opened by Colossus over 9 years ago
Labels: Distant supervision, Low priority, Dashboard / etc

#35 - Switch to DDLog

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

#35 - Switch to DDLog

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

#34 - P: add supervision rules based on dep path neighbors

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

#34 - P: add supervision rules based on dep path neighbors

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

#33 - Change config file to be ordered by entity

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

#33 - Change config file to be ordered by entity

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

#32 - Move delta-eval stuff to eval directory / separate out a bit?

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

#32 - Move delta-eval stuff to eval directory / separate out a bit?

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

#31 - Repo cleanup: onto directory, delete archived, util code, etc

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

#31 - Repo cleanup: onto directory, delete archived, util code, etc

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

#30 - Update to new Charite dataset

Issue - State: closed - Opened by ajratner over 9 years ago - 6 comments
Labels: Data source

#30 - Update to new Charite dataset

Issue - State: closed - Opened by ajratner over 9 years ago - 6 comments
Labels: Data source

#29 - Incorporate datasets beyond PLoS, PMC and PubMed

Issue - State: closed - Opened by ajratner over 9 years ago - 8 comments
Labels: Data source

#29 - Incorporate datasets beyond PLoS, PMC and PubMed

Issue - State: closed - Opened by ajratner over 9 years ago - 8 comments
Labels: Data source

#28 - Switch from fixed PLoS ID -> PMID dictionary to direct from XML

Issue - State: closed - Opened by ajratner over 9 years ago
Labels: Low priority, Data source

#28 - Switch from fixed PLoS ID -> PMID dictionary to direct from XML

Issue - State: closed - Opened by ajratner over 9 years ago
Labels: Low priority, Data source

#27 - [Mindtagger] Put all the other extractions in same sentence in

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

#27 - [Mindtagger] Put all the other extractions in same sentence in

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

#26 - [Mindtagger] Dependency path visualizations

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

#26 - [Mindtagger] Dependency path visualizations

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

#25 - GP: Can we use NHGRI GWAS catalogue / other similar datasets?

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: Distant supervision, Low priority, Data source

#25 - GP: Can we use NHGRI GWAS catalogue / other similar datasets?

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: Distant supervision, Low priority, Data source

#24 - P: Get rid of some bad phenos still showing up e.g. "chronic"

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

#24 - P: Get rid of some bad phenos still showing up e.g. "chronic"

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

#23 - Build a bit of light wrapper code for switching between doc section types?

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

#23 - Build a bit of light wrapper code for switching between doc section types?

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

#22 - [deepdive] Implement ScopedMultinomial / non-heuristic ENTITY LINKING...?

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: Candidate extraction, For later...

#22 - [deepdive] Implement ScopedMultinomial / non-heuristic ENTITY LINKING...?

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: Candidate extraction, For later...

#21 - Finish moving raw PMC data -> dfs

Issue - State: closed - Opened by ajratner over 9 years ago - 6 comments
Labels: Low priority, Data source

#21 - Finish moving raw PMC data -> dfs

Issue - State: closed - Opened by ajratner over 9 years ago - 6 comments
Labels: Low priority, Data source

#20 - G: Add in Generifs dataset for additional supervision?

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

#20 - G: Add in Generifs dataset for additional supervision?

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

#19 - G: Handling gene names that are part of multi-word proper nouns

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

#19 - G: Handling gene names that are part of multi-word proper nouns

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

#18 - G: Get rid of certain 'bad' gene names

Issue - State: closed - Opened by ajratner over 9 years ago - 3 comments
Labels: bug, Distant supervision, Data source

#18 - G: Get rid of certain 'bad' gene names

Issue - State: closed - Opened by ajratner over 9 years ago - 3 comments
Labels: bug, Distant supervision, Data source

#17 - G: Add some targeted distant supervision rules

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

#17 - G: Add some targeted distant supervision rules

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

#16 - Write DepPathDAG test extractor

Issue - State: closed - Opened by Colossus over 9 years ago - 2 comments

#16 - Write DepPathDAG test extractor

Issue - State: closed - Opened by Colossus over 9 years ago - 2 comments

#15 - Hook G & P up to config.py

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

#15 - Hook G & P up to config.py

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

#14 - Transition to new deepdive release

Issue - State: closed - Opened by ajratner over 9 years ago - 6 comments
Labels: Low priority

#13 - Set up eval against saved mindtagger labels (shell scripts + Dashboard)

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

#12 - Get eval against Charite/OMIM set working in Dashboard

Issue - State: closed - Opened by ajratner over 9 years ago
Labels: Dashboard / etc

#11 - GP: Work on handling negation / hypothetical statements better!

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

#10 - Integrate UMLS

Issue - State: closed - Opened by ajratner over 9 years ago - 1 comment
Labels: Candidate extraction, Data source, For later...

#9 - Add in genetic variant tagging (as preprocessing step)

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

#8 - Add a Defined Acronym extractor, use this to avoid incorrect G extractions

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

#7 - Too many negatively supervised GP examples from e.g. "associated"/"correlated" rules?

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

#6 - Genepheno mp

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

#5 - Dashboard integration

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

#4 - shell script to build gene mentions to ensembl mapping

Pull Request - State: closed - Opened by Mpaull almost 10 years ago

#3 - Simplify the gene mention extractor

Pull Request - State: closed - Opened by amwenger almost 10 years ago

#2 - instructions to build pmid_to_ensembl.tsv

Pull Request - State: closed - Opened by hguturu almost 10 years ago

#1 - Clean README and environment variable files

Pull Request - State: closed - Opened by amwenger almost 10 years ago - 1 comment

GitHub / hazyresearch/dd-genomics issues and pull requests