geneontology/neo

Issues

• add additional species names to gene labels

  #116 opened a year ago by balhoff
  6

• Add FB Developmental and Anatomy Ontology

  #117 opened 9 months ago by hattrill
  14

• Unknown reduction in entities in NEO build

  #118 opened 6 months ago by kltm
  15

• Ecoli data is gone from NEO as the upstream source changed

  #114 opened 2 years ago by kltm
  13

• unresolved IDs

  #106 opened 2 years ago by tmushayahama
  10

• In some cases bad identifiers are getting into the load

  #112 opened 2 years ago by kltm
  5

• Some e.coli entries not found

  #111 opened 2 years ago by pgaudet
  18

• Remove NEO build dependency on frozen datasets.json

  #58 opened 4 years ago by kltm
  1

• Many ChEBI chemicals not available for metabolic models

  #96 opened 2 years ago by marcfeuermann
  17

• RNAcentral IDs incorrectly use OBO PURL namespace

  #100 opened 2 years ago by balhoff
  5

• Xenbase identifiers are not correct getting labels (in NEO?)

  #109 opened 2 years ago by kltm
  5

• Add some minimal QC to the NEO pipeline

  #89 opened 2 years ago by kltm
  14

• Isoform display in label (originally on the visual tool)

  #102 opened 2 years ago by pmasson55
  4

• Would like phage proteins to be available

  #94 opened 2 years ago by dsiegele
  2

• Some IDs we expect are not found in Noctua

  #103 opened 2 years ago by pgaudet
  5

• Transient Xenbase issue dropped GPI file

  #104 opened 2 years ago by malcolmfisher103
  1

• Clarify and implement rules on inclusion of RNA gene products / RNA central

  #99 opened 2 years ago by cmungall
  4

• Request to load more phage proteins

  #95 opened 2 years ago by dsiegele
  2

• Xenbase entities do not seem to propagate to the NEO build from the Xenbase GPI

  #93 opened 2 years ago by kltm
  6

• Load all Swiss-Prot entries in NEO

  #82 opened 2 years ago by pgaudet
  22

• Trace entities that do not create nice URIs (i.e. compact well to CURIEs in out pipeline) in NEO

  #88 opened 2 years ago by kltm
  2

• Some Reactome Identifiers are not resolving

  #91 opened 2 years ago by ukemi
  11

• NEO GOlr / Solr load does not use "modern" loader, so does not build all closures for "modern" AmiGO

  #92 opened 2 years ago by kltm
  0

• Hacks in the NEO build process prevent branches from coexisting

  #86 opened 2 years ago by kltm
  1

• (Re)add sar-cov-2 GPI to NEO load

  #85 opened 2 years ago by kltm
  3

• load curated gpi file for sars-cov-2

  #60 opened 3 years ago by cmungall
  7

• Use ROBOT instead of owltools in NEO build

  #84 opened 3 years ago by kltm
  1

• ID / name collisions in ecocyc and goa_sars-cov-2 against uniprot_reviewed_virus_bacteria causing problem in NEO pipeline

  #80 opened 3 years ago by kltm
  16

• Include viruses and bacteria in NEO

  #77 opened 3 years ago by pgaudet
  26

• Load GPI file for UniProt reviewed entries for Virus and Bacteria in NEO

  #49 opened 3 years ago by pgaudet
  11

• Include Human Protein complexes in NEO

  #76 opened 3 years ago by pgaudet
  21

• ChEBI : limit load to ChEBI that have 'UniProt' synonyms

  #78 opened 3 years ago by pgaudet
  10

• Include Alliance automated gene descriptions as 'definitions' for gene entries

  #75 opened 3 years ago by vanaukenk
  3

• PRO ids map to more than one gene in PomBase gpi file - causing a neo build error

  #74 opened 3 years ago by vanaukenk
  33

• Model made in graph editor will not load into ART or Form

  #73 opened 3 years ago by hdrabkin
  25

• Check type of mouse ncRNA genes - not recognized in Noctua as valid annotation objects

  #72 opened 3 years ago by vanaukenk
  7

• MGI miRNA identifiers unavailable in NEO?

  #70 opened 3 years ago by vanaukenk
  22

• NEO no longer building

  #69 opened 3 years ago by kltm
  10

• Tweak obo-uris hack to handle hash injected by OBO parser

  #66 opened 3 years ago by kltm
  1

• Is NEO typing PRO identifiers correctly?

  #64 opened 4 years ago by vanaukenk
  5

• Some PR identifiers are not making it into the final (GOlr pipeline) product

  #51 opened 4 years ago by kltm
  12

• NEO no longer builds in the pipeline

  #62 opened 4 years ago by kltm
  15

• consider updating wormbase expansion

  #61 opened 4 years ago by balhoff
  3

• develop neo-lite for use in go-lego

  #47 opened 4 years ago by goodb
  4

• Roll out Xenopus Anatomy Ontology (XAO) for use in Noctua

  #59 opened 4 years ago by kltm
  2

• Need to check RGD identifiers in neo

  #52 opened 5 years ago by vanaukenk
  6

• ZFIN genes created in September 2019 and later are not available in Noctua (but available in our GPI)

  #53 opened 5 years ago by sabrinatoro
  14

• Identify test cases for NEO (and autocomplete) builds

  #54 opened 5 years ago by kltm
  1

• NEO no longer seems to build

  #50 opened 5 years ago by kltm
  7

• Create an is-a closure version of NEO for Noctua autocomplete

  #48 opened 5 years ago by vanaukenk
  2