v2.20.0

What's Changed

• 3 new provisional TR disease loci were added:
  • FAM193B and TBC1D7 are associated with OPDM
  • CEL is associated with MODY8
• Updates to the criTRia evidence descriptions and in some cases score adjustments for DAB1, NIPA, DMD, POLG, NAXE, and others with minor edits.
• New locus submission form fixed

Major Changes

• Add FAM193B and TBC1D7 by @Macayla-weiner in #352
• Add MODY8 locus again by @strchive-bot in #357

Minor Changes

• Add parse markdown util func by @vincerubinetti in #349
• fix locus form when adding new locus by @vincerubinetti in #354
• Naxe critria update by @hdashnow in #361
• Update Conflicting criTRia-curations.json by @Macayla-weiner in #363
• NIPA_ALS1-critria-update by @elbayaliyev in #366
• Update DAB1/SCA37 criTRia curation by @elbayaliyev in #360

Full Changelog: v2.19.0...v2.20.0

v2.19.0

What's Changed

• Simplify and validate criTRia format by @hdashnow in #345

Major Changes

• Merge Values, Evidence detail, and Notes into a single "Evidence
  details" field
• Create schema
• Validate format against schema
• Update score values as data is updated
• Add validation/update into Snakemake
• Round scores to the closest integer before comparing to classification ranges

Evidence category changes

Locus	Old category	New Category
FRA2A_AFF3	Moderate	Definitive
JBS_CBL	Strong	Definitive
SCA27B_FGF14	Strong	Definitive
HFG_HOXA13-II	Moderate	Limited
HFG_HOXA13-III	Moderate	Limited
NME_NAXE	Moderate	Limited
MRUPAV_PLIN4	Strong	Definitive
FAME2_STARD7	Moderate	Strong
FAME4_YEATS2	Moderate	Limited
HPE5_ZIC2	Moderate	Definitive

Minor Changes

• Fixes to curation data to make it valid with the new schema e.g. date
  formatting, citation formatting, and inheritance abbreviations.

Full Changelog: v2.18.0...v2.19.0

v2.18.0

What's Changed

• add association_type and evidence fields to STRchive-loci by @hdashnow in #332

Major Changes

• Number of criTRia curated loci increased from 55 to 74 (12 from ClinGen, 19 by @laurelhiatt and @Macayla-weiner)
• criTRia curations populated into STRchive locus pages
• Display improvements for curation data by @vincerubinetti
• Add provisional evidence category

Minor Changes

• Data cleanup and cross-links
• Auto-populate curations from criTRia
• Remove previous evidence tags

Full Changelog: v2.17.2...v2.18.0

v2.17.2

What's Changed

• Update Literature by @github-actions[bot] in #336
• April lit review + interruption data by @Macayla-weiner in #337

Minor Changes

• interruptions for NIPA1, NOTCH2NLC, SAMD12, FXN, FMR1, HTT, RILPL1,
  THAP11, ATXN1, ATXN 10, ATXN2, FGF14, ATXN3, NOP56, ATXN8OS, RAI1, and
  TBP
• RAI1 typo fixed

Related issues: #203 #286

Full Changelog: v2.17.1...v2.17.2

v2.17.1

What's Changed

• Update Literature by @github-actions[bot] in #326
• add interruption fields by @hdashnow in #335
• March Lit update by @Macayla-weiner in #334

Minor Changes

• ATXN2 intermediate range now 29-24
• ATXN2 locus details cleaned up to be a touch to be less repetitive
• SCA7 motif updated for clarity from GCA to CAG
• interruption field added to json (backwards compatible, not yet displayed)

Full Changelog: v2.17.0...v2.17.1

v2.17.0

What's Changed

Introducing "criTRia" locus-disease curations by @Macayla-weiner and @laurelhiatt. This version introduces the framework and a first draft of curations for 55 loci. More detail and curations to follow.

Major Changes

• criTRia page by @hdashnow and @vincerubinetti in #328

Full Changelog: v2.16.0...v2.17.0

v2.16.0

What's Changed

• fix refs by @hdashnow in #315
• print new literature to file by @hdashnow in #320
• Update Literature by @github-actions[bot] in #321
• Feb lit update + additional PRs by @Macayla-weiner in #324

Fixes: #318 , #295 , #317 , #284. #322, #319, #308

Major Changes

• FTDALS1 pathogenic minimum brought down to 31 (intermediate brought down to 30)
• Updating outdated "mental retardation" to "intellectual development disorder" in FRAXE (#318), FXS, & XMLR
• AFF2 name change (#318 ) and incomplete list of HPO terms added
• XLMR name change and disease ID change to XID
• New mechanistic information for OPDM2 (#295)
• Additional name added to NIID (#317)
• Handful of Motifs added to RFC1 (#322)

Minor Changes

• FMR1 gene updated to fragile X messenger ribonucleoprotein 1 in FXS description
• Added phenotype for premutation to FXTAS
• Additional mechanism detail added to NIID
• Added phenotype to CCHS

Full Changelog: v2.15.0...v2.16.0

v2.15.0

What's Changed

• Jan lit update by @Macayla-weiner in #313 and #307

Major Changes

Complex expansion of FGF14 has been implicated as a Parkinson's risk factor in two articles

Minor Changes

Grammar fixes to FTD_ALS and CSTB_EMP1

Code updates

• Fix long motifs in loci table by @vincerubinetti in #305
• change get-literature.R to use rentrez only instead of easyPubMed by @hdashnow in #306

Full Changelog: v2.14.0...v2.15.0

v2.14.0

What's Changed

• November literature update by @Macayla-weiner and @hdashnow

Major Changes

Code updates

• update pubmed fetch code by @hdashnow in #292 (this changes the filenames for the literature .txt. medline files
• switch scheduled workflow back to long by @hdashnow in #299

Minor Changes

Locus updates

• Update citations by @hdashnow in #291

• RFC1 in PD by @Macayla-weiner in #297

• ATN1 Lit Update by @Macayla-weiner in #293

• C9orf72 PD association by @Macayla-weiner in #294

• OPDM1 Mechistic info by @Macayla-weiner in #296

• update version by @hdashnow in #300

Full Changelog: v2.13.0...v2.14.0

v2.13.0

What's Changed

October literature update by @Macayla-weiner and @hdashnow

Major Changes

• MARCHF6 lower pathogenic size threshold by @Macayla-weiner #282

Minor Changes

• ADTKD lower onset bound by @Macayla-weiner in #285
• October literature update by @hdashnow in #283

Full Changelog: v2.12.0...v2.13.0