Commits · 05fd7e53b0de202879d276378c101665724e0172 · ensembl-gh-mirror / ensembl

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Jun 25, 2012
- populate xref description with ensembl object description if the xref... · 05fd7e53
  Monika Komorowska authored 12 years ago
```
populate xref description with ensembl object description if the xref description is empty and copy_description_from_object parameter is true
```
  05fd7e53
- store description instead of accession in the label field... · c85cdf18
  Monika Komorowska authored 12 years ago
```
store description instead of accession in the label field http://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-180
```
  c85cdf18
- don't parse Orphanet xrefs from UniProt http://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-180 · 9395ce34
  Monika Komorowska authored 12 years ago
  
  9395ce34
Jun 22, 2012
- load registry in the main parser · 50996c8c
  Monika Komorowska authored 12 years ago
  
  50996c8c
- Ensembl version of the RFAMParser is not needed · ed1645c7
  Monika Komorowska authored 12 years ago
  
  ed1645c7
- RFAM xrefs need to be parsed using CoreXrefParser for EnsemblGenomes · 931f34a4
  Monika Komorowska authored 12 years ago
  
  931f34a4
- RFAMParser which loads the registry with EnsemblGenomes databases · eb20db7a
  Monika Komorowska authored 12 years ago
  
  eb20db7a
- generic RFAMParser which RFAMParser_E and RFAMParser_EG inherit from · 4749b9f8
  Monika Komorowska authored 12 years ago
  
  4749b9f8
- RFAMParser which loads the registry with EnsEMBL databases · d8a1585c
  Monika Komorowska authored 12 years ago
  
  d8a1585c
- parser for xrefs from core which are generated by an analysis straight into a core db · 08911acf
  Monika Komorowska authored 12 years ago
  
  08911acf
Jun 21, 2012
- deleted unnecessary module import · e171eaab
  Monika Komorowska authored 12 years ago
  
  e171eaab
- fix module name · 2e97bb88
  Monika Komorowska authored 12 years ago
  
  2e97bb88
- RFAM parser for ensembl genomes · df160679
  Monika Komorowska authored 12 years ago
  
  df160679
Jun 20, 2012
- fixed output message · 2e4b0861
  Monika Komorowska authored 12 years ago
  
  2e4b0861
- new parser for RFAM xrefs, replaces use of ncRNA_DBParser in ensembl · 35cf179e
  Monika Komorowska authored 12 years ago
  
  35cf179e
- new parser for miRBase xrefs, replaces use of ncRNA_DBParser in ensembl · 3c361f02
  Monika Komorowska authored 12 years ago
  
  3c361f02
Jun 11, 2012
- another attempt to accommodate multiple ensembl stable ids linking to the same vega stable id · fce7e886
  Monika Komorowska authored 12 years ago
  
  fce7e886
Jun 08, 2012
- fix splitting of synonyms · 41090d4b
  Monika Komorowska authored 12 years ago
  
  41090d4b
- amended header_template value, description and printing of synonym counts · ceec6b24
  Monika Komorowska authored 12 years ago
  
  ceec6b24
Jun 01, 2012
- Adapted to use new file format, with combined the synonyms. · 2adede1f
  Kieron Taylor authored 12 years ago
  
  2adede1f
May 15, 2012
- ENSCORESW-138. Fixed the encoded entities by de-encoding them. Code is... · 7f00be87
  Andy Yates authored 12 years ago
```
ENSCORESW-138. Fixed the encoded entities by de-encoding them. Code is untested though and should be treated with caution
```
  7f00be87
Apr 27, 2012
- Do not quote identifiers if they are going into a prepared statement.... · d5c007fe
  Andy Yates authored 12 years ago
```
Do not quote identifiers if they are going into a prepared statement. Otherwise we end up with odd results
```
  d5c007fe
Apr 18, 2012
- Append accession number to the display label. · 15e78dcf
  Monika Komorowska authored 12 years ago
```
JIRA ticket: http://www.ebi.ac.uk/panda/jira/browse/ENSCORESW-117
```
  15e78dcf
Apr 16, 2012
- don't strip off the SSF prefix · 101e1369
  Monika Komorowska authored 12 years ago
  
  101e1369
Apr 13, 2012
- file format changed · c9f97ac6
  Monika Komorowska authored 12 years ago
  
  c9f97ac6
Apr 10, 2012
- Removed problematic (!defined $release_file) test. · 0efe34de
  Derek Wilson authored 12 years ago
  
  0efe34de
Apr 04, 2012
- changes to accommodate multiple ensembl stable ids linking to the same vega stable id · 08998c86
  Monika Komorowska authored 12 years ago
  
  08998c86
Mar 29, 2012
- don't store digits in type · 48a0078f
  Monika Komorowska authored 12 years ago
  
  48a0078f
Mar 27, 2012
- changes for xrefs with evidence > 2 · 93e29f8b
  Monika Komorowska authored 12 years ago
  
  93e29f8b
- select transcripts only to get rid of duplicate sql query results · 613ee0e2
  Monika Komorowska authored 12 years ago
  
  613ee0e2
- escape underscores so they are not treated as a wildcard character · 94f7ff7c
  Monika Komorowska authored 12 years ago
  
  94f7ff7c
Mar 19, 2012
- Changed the WormBase-specfic functionality to better match the data · b65dfc28
  Kevin Howe authored 13 years ago
  
  b65dfc28
Mar 14, 2012
- Updated WormBase direct xrefs · 858eb892
  Kevin Howe authored 13 years ago
  
  858eb892
Feb 22, 2012

Attempting to fix the issues with too many KNOWN status genes appearing in... · 0fe32d38

Andy Yates authored 13 years ago

Attempting to fix the issues with too many KNOWN status genes appearing in species we should not be seeing them in. UniProtParser now limits to using ACs with an evidence of 1 and 2. We now do not assign KNOWN based upon a depdendent xref when we didn't trust the parent xref. Also the loader & SQL has been edited to allow for LOWEVIDENCE types of sources.

0fe32d38

Bringing the bit after # back in · a5643444
Andy Yates authored 13 years ago

a5643444

Feb 15, 2012
- new parser for Orphanet xrefs dependent on HGNC identifiers · 07a96f2a
  Monika Komorowska authored 13 years ago
  
  07a96f2a
Feb 07, 2012
- Module associated with the Broad Magnaporthe Comparative DB; inherits fro mthe... · b6bd2b48
  Arnaud Kerhornou authored 13 years ago
```
Module associated with the Broad Magnaporthe Comparative DB; inherits fro mthe generic broad parser, Broad_GenericParser.pm
```
  b6bd2b48
- Broad generic parser; needs to be superseded by another module in order to get the right source_id · a5b960ca
  Arnaud Kerhornou authored 13 years ago
  
  a5b960ca
Jan 12, 2012
- set status for parser to failed if no xrefs found · c4fb2de4
  Monika Komorowska authored 13 years ago
  
  c4fb2de4
Jan 10, 2012
- Added specific code for Scer for parsing the EC number from the description line · 6d0eae0f
  Arnaud Kerhornou authored 13 years ago
  
  6d0eae0f