Recent Releases of BED
BED - Version 1.2.3
Version 1.2.3 - Release notes - 2020-01-24
Rebuild-BED.Rmd
- Ensembl 99
- Based on neo4j-community-3.5.14
- NCBI does not support mapping to unigene and vega anymore. Unigene and Vega identifiers are not available anymore in BED as well.
Implementation changes
- Prepopulate nodes with a subset and use 'CALL db.resampleOutdatedIndexes();' to speed up the feeding process.
- R
Published by patzaw over 6 years ago
BED - Version 1.2.2
Version 1.2.2 - Release notes - 2019-10-13
Implementation changes
- Correction of findBe() result display
- Correction of bug in getBeIds() and getRelevantIds()
- Implement BEIDList class
- cleanDubiousXRef() function applied to NCBI gene cross-references from Ensembl
- Improving mapping function for supporting difficult history of Zebrafish Ensembl identifiers
Rebuild-BED.Rmd
- Based on neo4j-community-3.5.11
- Ensembl 98
- Add Danio rerio (zebrafish) support
- Because of a few (a very small number but quite annoying) dubious mapping
with EntrezGene identifier, only unambigous mapping from Ensembl have been
conserved. Relevant ambigous mapping be rescued by mapping from the NCBI
and to other reference database such as HGNC, MGI or RGD.
The cleanDubiousXRef() has been updated to this end
Examples:
- https://www.ensembl.org/Homo_sapiens/Gene/Matches?g=ENSG00000120088
- R
Published by patzaw over 6 years ago
BED - Version 1.1.8
Version 1.1.8 - Release notes - 2019-07-29
Implementation changes
- Correction of how Ensembl data files are pre-processed because of the apparition of "carriage return" (\r\n) characters.
- Give write rights on the neo4j database before copying it in the docker image.
Rebuild-BED.Rmd
- Based on neo4j-community-3.5.7
- Ensembl 97
Version 1.1.7 - Release notes - 2019-05-08
Implementation changes
- When associating one id to another, the BE identified by the first id is deleted after that its production edges have been transferred. After this operation all id "corresponding_to" the first id do not directly identify any BE as they should be supposed to do. Thus, it's not recommended to associate such ID to others.
Version 1.1.6 - Release notes - 2019-04-23
Implementation changes
- Split the toImport file in the bedImport function before loading csv in neo4j ==> improve robustness and efficiency of the load
- Separate import of nodes and import of edges to avoid neo4j eager issues
- Add Sus scrofa support in the dumpUniprotDb function
- Ensembl history has been adapted to avoid loop (found for some pig transcripts)
Rebuild-BED.Rmd
- Based on neo4j-community-3.5.4
- Ensembl 96
- Add GPL6887 platform
- Add Sus scrofa (pig) support
- Set the following cypher parameters during the building to avoid query
replanning (https://neo4j.com/blog/cypher-write-fast-furious/):
- --env=NEO4Jcypherminreplaninterval=100000000ms \
- --env=NEO4Jcypherstatisticsdivergencethreshold=1 \
- R
Published by patzaw almost 7 years ago
BED - Version 1.1.5
Methodological changes
- Improving case insentive conversion from and to symbols
Rebuild-BED.Rmd
- Based on neo4j-community-3.4.12
- Ensembl 95
- R
Published by patzaw over 7 years ago
BED - Version 1.1.4
- Notes about converting from and to gene symbols in the BED vignette.
- Simplification of the feeding procedure based on docker (see README.md)
- R
Published by patzaw almost 8 years ago