TranslatorSRI/Babel

Issues

• RXCUI:1736859 "insulin glargine 100 UNT/ML [Basaglar]" not combined with other insulins

  #356 opened 2 months ago by gaurav
  0

• Issues with NameResolver identifying Simoctocog Alfa

  #354 opened 2 months ago by marcello-deluca
  1

• Number of GeneProtein conflations and fell in 2024oct1

  #355 opened 2 months ago by gaurav
  1

• Improve Babel CPU and memory configuration on Sterling

  #353 opened 2 months ago by gaurav
  0

• Improve PubMed download

  #352 opened 2 months ago by gaurav
  0

• How do we deal with the different types of insulin?

  #327 opened 4 months ago by gaurav
  4

• Figure out how to use the identically-labeled-clique information to make things better

  #338 opened 3 months ago by gaurav
  1

• Missing gene connection with UMLS because we don't include NCIT mappings

  #350 opened 3 months ago by gaurav
  1

• Check Drug.txt to ensure that we don't have small molecules in there

  #348 opened 3 months ago by gaurav
  0

• Should bivalirudin and bivalirudin trifluoroacetate be cliqued together?

  #346 opened 3 months ago by gaurav
  0

• Some genes have bad preferred names, but preferred prefix boosting might help

  #312 opened 5 months ago by gaurav
  1

• NCBIGenes missing primary label

  #345 opened 3 months ago by gaurav
  0

• Brand name "Estrostep Fe" not tied to the underlying PubChem

  #344 opened 3 months ago by gaurav
  0

• Xylitol - split clique

  #343 opened 3 months ago by gaurav
  0

• DrugBank ID being dropped between untyped compendium and final ChemicalEntity compendium

  #332 opened 3 months ago by gaurav
  2

• DrugChemical conflation defaults to the numerically smallest identifier, which doesn't always work

  #341 opened 3 months ago by gaurav
  0

• Missing some human proteins, even though we have the genes for them

  #339 opened 3 months ago by gaurav
  0

• Downscore labels which are very long or look like chemical names

  #313 opened 5 months ago by gaurav
  0

• Label chosen as per preferred label prefixes for chemicals doesn't always return the best name

  #306 opened 5 months ago by gaurav
  1

• Some entities are showing up in both proteins and chemicals

  #310 opened 5 months ago by gaurav
  1

• some curies that probably should be linked

  #333 opened 4 months ago by gglusman
  1

• Implement a species conflation

  #334 opened 4 months ago by gaurav
  0

• Include labels from DrugBank?

  #317 opened 5 months ago by gaurav
  2

• Watch out for conflation issues with labeling

  #331 opened 4 months ago by gaurav
  0

• Improved and more transparent cliquing

  #326 opened 4 months ago by gaurav
  0

• Babel technical debt

  #323 opened 4 months ago by gaurav
  0

• "Organism" class in LitCoin covers many types of concepts, some of which we don't have

  #324 opened 4 months ago by gaurav
  0

• Improve choice of the best preferred identifier for conflated chemicals

  #322 opened 4 months ago by gaurav
  0

• Prefix OMIM should be renamed to MIM

  #321 opened 4 months ago by gaurav
  0

• Carbon has a preferred label of "activated charcoal"

  #304 opened 5 months ago by gaurav
  0

• Publish intermediate files or other information to explain how we came to our cliquing decisions

  #319 opened 5 months ago by gaurav
  0

• Different preferred labels with and without drug conflation

  #318 opened 5 months ago by gaurav
  0

• Improve prioritization

  #316 opened 5 months ago by gaurav
  0

• Types ordering in NameRes a little odd

  #315 opened 5 months ago by gaurav
  0

• Improve conflation for combinations like paxlovid or augmentin

  #314 opened 5 months ago by gaurav
  0

• Chembl identifiers aren't being properly connected to other entities

  #311 opened 5 months ago by gaurav
  0

• Add manual concords for other types

  #309 opened 5 months ago by gaurav
  0

• Some UMLS-MeSH connections are broken in Babel 2024jul13

  #308 opened 5 months ago by gaurav
  0

• PUBCHEM.COMPOUND:162343947 causing problems in drugchemical conflation in the current run

  #307 opened 5 months ago by gaurav
  0

• Glimepiride has a long chemical name despite the alternate label algorithm

  #289 opened 6 months ago by gaurav
  0

• Should NCIT be an allowed prefix for proteins?

  #305 opened 5 months ago by gaurav
  0

• Do a better job of cliquing inadequatelly mapped UMLS identifiers

  #302 opened 5 months ago by gaurav
  1

• Some concepts are being assigned to the wrong category

  #299 opened 5 months ago by gaurav
  0

• Get synonyms-per-clique distribution

  #301 opened 5 months ago by gaurav
  0

• Why is `NCBITaxon:family` in Babel?

  #298 opened 6 months ago by gaurav
  0

• Incorporate LOINC into Babel

  #295 opened 6 months ago by gaurav
  0

• Store alternate type information in addition to Biolink types

  #294 opened 6 months ago by gaurav
  0

• Golgi apparatus split

  #293 opened 6 months ago by gaurav
  0

• Replace the in-memory glomming code with DuckDB databases

  #291 opened 6 months ago by gaurav
  0

• Lots of acetaminophens still not conflated with the main acetaminophen

  #288 opened 6 months ago by gaurav
  0