Releases: ncats/RaMP-DB
v2.3.4
This patch release has an update to chemical class survey and enrichment. The query sql had to be modified to be compatible with MySQL v8+ installations where the sql_mode ONLY_FULL_GROUP_BY is set and enforced. Certain chemical class survey and enrichment queries would fail. The sql has been updated to correct this issue.
v2.3.3
This patch release has the following improvements:
- The pathway enrichment code has been enhanced to improve performance on large input analyte lists, decreasing execution time by roughly 60%.
- This release also features Rhea Reaction queries where analyte lists consisting of proteins, metabolites or a combination of both can be entered, resulting in a list of associated Rhea Reactions. The result of this query will be a set of three reaction lists, one for reactions associated with metabolites, one reaction list associated with entered genes or proteins, and one reaction list that lists reactions that are in common. The reactions in this third list will list reactions in which there is an association with at least on metabolite and one protein from the input list.
v2.3.2
v2.3.1
v2.3.1:
• Optimized biological pathway enrichment methods to improve performance speed. The API method (api/combined-fisher-test) and the RaMP Web utility (Biological Pathway Enrichment) will see faster response times for enrichment analyses.
• getAnalyteFromPathways() now takes as input a list of pathway ids (e.g., WP2788 or R-HSA-428157) in addition to pathway names.
• getAnalyteFromPathways() now outputs a 'pathwayId' field in the returned table of analyte information.
• FilterFishersResults() has been patched for a problem that could occur when running versions of R > 4.3 (due to '&&' no longer being supported by new R version).
v2.3.0
- Performance/speed improvements to pathway enrichment, runCombinedFisherTest()
- getAnalyteFromPathway() function changed to support searching by pathway IDs (request from Translator) and has been modified to return pathway IDs.
- This version still uses version 2.2.1 of the database (https://figshare.com/ndownloader/files/39460683).
v2.2.1
RaMP v2.2.1 is a database refresh update and data curation release.
The latest release includes additional records for LIPID MAPS, ChEBI, and WikiPathways. Releases input are:
- HMDB v5.0 (2021-11-17)
- Reactome v83 (Nov 2022)
- WikiPathways v20230210 (2023-02-10)
- KEGG from HMDB (v5.0) (2021-11-17)
- ChEBI Release 218 (2022-02-01)
- LidpidMAPS Release 2023-02-24
New data curation included removal of 320 metabolite id cross-reference errors found in source data. Curation is used to identify metabolite ID type cross references from data sources that incorrectly link unrelated compounds. Automated first-pass curation includes an initial check based on the monoisotopic mass associated with the ID pair being tested. ID pairs with masses that differ by greater than 10% from the smaller mass are send to a log for manual curation where verified mis-mappings are added to an exclusion list used to stop the propagation of improper ID cross references. In this build an additional step was introduced to query the chemical properties table in the RaMP database to discover additional bad ID pair cross-references that were missed by the process due to incomplete mass information for certain ID types. A second round of manual curation is used to resolve remaining ID cross reference errors.
v2.2.0
Data refresh includes addition of secondary HMDB ids, updated harmonization using collapsing on inchi-key prefix.
The corresponding database v2.2.0 is on figshare - https://figshare.com/ndownloader/files/38534654
*Note: the README will always have the latest version linked.
RaMP_v2.0.7_20220504
RaMP 2.0 is now released and includes an updated backend database with expanded annotations for >150,000 metabolites and ~14,000 genes/proteins. Annotations include biological pathways, chemical classes and structures (for metabolites only), ontologies (metabolites only), and enzyme-metabolite relationships based on chemical reactions. Annotations are drawn from HMDB, KEGG (through HMDB), Lipid-MAPS, WikiPathways, Reactome, and ChEBI.
RaMP Version 1 Stable Release (v.1.2.0)
This version is stable and includes all the functionalities associated with the first RaMP publication (https://pubmed.ncbi.nlm.nih.gov/29470400/), which includes the backend database, R package, and RShiny App. The underlying RaMP database is dated from 03/02/2018. Code was updated to support moving the project over to NCATS and deploying the Shiny App on NCATS servers. The R Shiny server is now deprecated but the Shiny App can still be run locally.