dkoslicki/NCATS

Issues

• regression test suite

  #131 opened 7 years ago by saramsey
  1

• Look into Cy2neo for neo4j visualization

  #101 opened 7 years ago by saramsey
  3

• [LOWPRI] Why is Orangeboard executing Cypher statements in a transaction?

  #88 opened 7 years ago by saramsey
  28

• test the proof-of-concept OpenAPI interface for RTX

  #95 opened 6 years ago by saramsey
  3

• Random Walk with Restart development

  #98 opened 6 years ago by saramsey
  3

• Check results of Q2Solution.py

  #107 opened 6 years ago by dkoslicki
  2

• Add code for Timeout handling to QueryReactome

  #115 opened 6 years ago by saramsey
  1

• Web service should return reusable (structured) results

  #116 opened 6 years ago by edeutsch
  5

• change "pharos_drug" to "drug" in BioNetExpander, BuildMasterKG, and Q2Utils.py

  #117 opened 6 years ago by saramsey
  1

• Write QueryJASPAR class to query JASPAR's REST API

  #126 opened 6 years ago by saramsey
  1

• Connection issue for Neo4j on ncats.saramsey.org

  #128 opened 6 years ago by saramsey
  1

• add MeSH definitions into the knowledge graph

  #132 opened 6 years ago by saramsey
  1

• add ChEMBL drug->target probability scores for target predictions to the KG

  #133 opened 6 years ago by saramsey
  1

• Geneprof 500 response

  #134 opened 6 years ago by erikyao
  1

• update BuildMasterKG.py to seed all FDA-approved drugs

  #130 opened 7 years ago by saramsey
  0

• 404 error in BuildMasterKG.get_curie_ont_ids_for_mesh_term

  #129 opened 7 years ago by saramsey
  0

• Write command-line script for PubMed NGD semantic distance calculation

  #127 opened 7 years ago by saramsey
  0

• Test out WebEx logistics from Bexell 211

  #114 opened 7 years ago by saramsey
  8

• -Inf in Q2Solution.py confidence

  #108 opened 7 years ago by dkoslicki
  2

• JSON issue with null result from Q1

  #125 opened 7 years ago by saramsey
  4

• http://ncats.saramsey.org/doc/RTX/index.html returns 404

  #123 opened 7 years ago by erikyao
  6

• for JSON output from Q1Solution, add "text" field with human-readable text

  #124 opened 7 years ago by saramsey
  3

• test Q1 command-line-interface script

  #96 opened 7 years ago by saramsey
  0

• Easy-to-implement suggestions for the web UI

  #97 opened 7 years ago by saramsey
  0

• add JSON output format as a command-line option in Q1Solution.py

  #122 opened 7 years ago by saramsey
  0

• write howto on deploying RTX POC via docker

  #118 opened 7 years ago by saramsey
  1

• Backup SQLite cache, neo4j database, and docker image to S3

  #90 opened 7 years ago by saramsey
  2

• Orangeboard.py not closing Neo4j session

  #121 opened 7 years ago by saramsey
  0

• Normalized Google Distance matrix based on PubMed abstract full-text search (Q1)

  #99 opened 7 years ago by saramsey
  1

• Configure lysine.ncats.io Neo4j instance to be read-only

  #119 opened 7 years ago by saramsey
  1

• Error when calling QXSolution -h, X=1,2

  #120 opened 7 years ago by dkoslicki
  3

• Make HTML mockup showing PubMed literature co-occurrence analysis

  #93 opened 7 years ago by saramsey
  1

• Please help review the Google Slides presentation on Tuesday 11/28

  #94 opened 7 years ago by saramsey
  1

• only 656 out of 1000 drugs are mapped to a target protein

  #102 opened 7 years ago by saramsey
  3

• Readme in UI directory

  #113 opened 7 years ago by dkoslicki
  1

• Duplicate PC2 protein-protein interaction edges in the KG when exported to CSV

  #104 opened 7 years ago by saramsey
  3

• API caching for Q1 and Q2?

  #112 opened 7 years ago by dkoslicki
  8

• Full results not printing

  #109 opened 7 years ago by dkoslicki
  0

• Q2 multi-word diseases

  #105 opened 7 years ago by dkoslicki
  3

• Catching NCBI eUtils timeout

  #111 opened 7 years ago by dkoslicki
  5

• disease/drug not in Q2 list

  #106 opened 7 years ago by dkoslicki
  0

• password-protect TCP port 80 access on lysine.ncats.io and ncats.saramsey.org

  #103 opened 7 years ago by saramsey
  1

• How many drugs in our KG are connected to proteins?

  #91 opened 7 years ago by saramsey
  1

• put MIT LICENSE file in the code directory

  #100 opened 7 years ago by saramsey
  0

• check q2-drugandcondition-list-mapped.txt into GitHub to Q2 tool can use it

  #92 opened 7 years ago by saramsey
  1

• Need a script to dump Neo4j database to CSV/TSV

  #89 opened 7 years ago by saramsey
  0

• make Neo4j database on lysine read-only

  #87 opened 7 years ago by saramsey
  1

• add HTTP caching to Q1Solution.py

  #85 opened 7 years ago by saramsey
  1

• make the number of expansions in BuildMasterKG.seed_and_expand_kg_q1[q2] configurable

  #86 opened 7 years ago by saramsey
  0

• cleanup git repo

  #84 opened 7 years ago by saramsey
  1