From dae7ecfa7b20bb955388f11da4db6907753bbb34 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Fri, 26 Apr 2024 17:16:49 -0400 Subject: [PATCH 1/3] First stab at adding release notes for Translator May 2024. --- releases/README.md | 5 +++-- releases/TranslatorDecember2023.md | 4 ++-- releases/TranslatorMay2024.md | 15 +++++++++++++++ 3 files changed, 20 insertions(+), 4 deletions(-) create mode 100644 releases/TranslatorMay2024.md diff --git a/releases/README.md b/releases/README.md index a75ce391..05d6740d 100644 --- a/releases/README.md +++ b/releases/README.md @@ -2,5 +2,6 @@ ## Translator Releases -- [October 2023](TranslatorOctober2023.md) -- [December 2023](TranslatorDecember2023.md) \ No newline at end of file +- [May 2024](TranslatorMay2024.md) +- [December 2023](TranslatorDecember2023.md) +- [October 2023](TranslatorOctober2023.md) \ No newline at end of file diff --git a/releases/TranslatorDecember2023.md b/releases/TranslatorDecember2023.md index 838267f9..60812ed6 100644 --- a/releases/TranslatorDecember2023.md +++ b/releases/TranslatorDecember2023.md @@ -1,9 +1,9 @@ # NameRes Translator December 2023 Release - Babel: [2023nov5](https://stars.renci.org/var/babel_outputs/2023nov5/) -- NameRes: [v2.3.11](https://github.com/TranslatorSRI/NameResolution/releases/tag/v1.3.11) +- NameRes: [v1.3.11](https://github.com/TranslatorSRI/NameResolution/releases/tag/v1.3.11) -Next release: _None as yet_ +Next release: [Translator May 2024](TranslatorMay2024.md) ## New features * The `/lookup` endpoints now: diff --git a/releases/TranslatorMay2024.md b/releases/TranslatorMay2024.md new file mode 100644 index 00000000..3ecda77a --- /dev/null +++ b/releases/TranslatorMay2024.md @@ -0,0 +1,15 @@ +# NameRes Translator May 2024 Release + +- Babel: [2024mar24](https://stars.renci.org/var/babel_outputs/2024mar24/) +- NameRes: [v1.3.12](https://github.com/TranslatorSRI/NameResolution/releases/tag/v1.3.12) + +Next release: _None as yet_ + +## New features +* Solr database now has two additional fields for each clique: + * `taxa`: list of taxa that a clique is found in; in Babel 2024mar24, only NCBIGenes have taxa (as generated by + [TranslatorSRI/Babel#211](https://github.com/TranslatorSRI/Babel/pull/211)). + * `clique_identifier_count`: the number of identifiers in this clique (as generated by + [TranslatorSRI/Babel#228](https://github.com/TranslatorSRI/Babel/pull/228)). +* The `/lookup` endpoints now return `taxa` and `clique_identifier_count`. They also have an `only_taxa` filter that + can be used to provide a pipe-delimited list of NCBITaxon entries to filter results with. From c19be193fa79883446c42672e2f719a65860deaa Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 29 Apr 2024 18:44:06 -0400 Subject: [PATCH 2/3] Added reference to the Babel Translator May 2024 release. I'll change that to a link after https://github.com/TranslatorSRI/Babel/pull/268 has been merged. --- releases/TranslatorMay2024.md | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/releases/TranslatorMay2024.md b/releases/TranslatorMay2024.md index 3ecda77a..a0d6879a 100644 --- a/releases/TranslatorMay2024.md +++ b/releases/TranslatorMay2024.md @@ -1,6 +1,5 @@ # NameRes Translator May 2024 Release - -- Babel: [2024mar24](https://stars.renci.org/var/babel_outputs/2024mar24/) +- Babel: [2024mar24](https://stars.renci.org/var/babel_outputs/2024mar24/) (Babel Translator May 2024 Release) - NameRes: [v1.3.12](https://github.com/TranslatorSRI/NameResolution/releases/tag/v1.3.12) Next release: _None as yet_ From eb57fdcd96ff4d90773362fd2949236f162ece88 Mon Sep 17 00:00:00 2001 From: Gaurav Vaidya Date: Mon, 29 Apr 2024 18:50:55 -0400 Subject: [PATCH 3/3] Added Babel updates to May 2024 release notes. --- releases/TranslatorMay2024.md | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/releases/TranslatorMay2024.md b/releases/TranslatorMay2024.md index a0d6879a..b3fc804e 100644 --- a/releases/TranslatorMay2024.md +++ b/releases/TranslatorMay2024.md @@ -12,3 +12,12 @@ Next release: _None as yet_ [TranslatorSRI/Babel#228](https://github.com/TranslatorSRI/Babel/pull/228)). * The `/lookup` endpoints now return `taxa` and `clique_identifier_count`. They also have an `only_taxa` filter that can be used to provide a pipe-delimited list of NCBITaxon entries to filter results with. + +## Babel updates (from Babel Translator May 2024 Release) +* [New identifiers] 36.9 million PubMed IDs (e.g. `PMID:25061375`) have been added as `biolink:JournalArticle`, as well as + the mappings to PMC (e.g. `PMC:PMC4109484`) and DOIs (e.g. `doi:10.3897/zookeys.420.7089`) that are included in PubMed. + Details in [TranslatorSRI/Babel#227](https://github.com/TranslatorSRI/Babel/pull/227). +* Fixed type determination for DrugChemical conflation. Details in + [TranslatorSRI/Babel#266](https://github.com/TranslatorSRI/Babel/pull/266). +* Synonym files now include the clique identifier count (the number of identifiers in each clique) in synonyms file. +* Minor fixes.