Commit 918bc2ab authored by carlosribas's avatar carlosribas
Browse files

Set up piRBase

parent b0b98858
......@@ -91,7 +91,7 @@ expert_dbs = [
],
'imported': True,
'status': 'updated',
'version': 'as of July 20th, 2020',
'version': 'as of December 20th, 2020',
},
{
'name': 'FlyBase',
......@@ -116,7 +116,7 @@ expert_dbs = [
],
'imported': True,
'status': 'updated',
'version': 'FB2020_03',
'version': 'FB2020_06',
},
{
'name': 'Ensembl',
......@@ -147,7 +147,7 @@ expert_dbs = [
],
'imported': True,
'status': 'updated',
'version': '100',
'version': '102',
},
{
'name': 'Ensembl Plants',
......@@ -172,7 +172,7 @@ expert_dbs = [
],
'imported': True,
'status': 'updated',
'version': '47',
'version': '49',
},
{
'name': 'Ensembl Fungi',
......@@ -197,7 +197,7 @@ expert_dbs = [
],
'imported': True,
'status': 'updated',
'version': '47',
'version': '49',
},
{
'name': 'Ensembl Metazoa',
......@@ -222,7 +222,7 @@ expert_dbs = [
],
'imported': True,
'status': 'updated',
'version': '47',
'version': '49',
},
{
'name': 'Ensembl Protists',
......@@ -247,11 +247,11 @@ expert_dbs = [
],
'imported': True,
'status': 'updated',
'version': '47',
'version': '49',
},
{
'name': 'GENCODE',
'label': 'gencode',
'name': 'Ensembl/GENCODE',
'label': 'ensembl_gencode',
'url': 'http://gencodegenes.org/',
'description': 'produces high quality reference gene annotation and experimental validation for human and mouse genomes',
'hint': 'GENCODE produces high quality reference gene annotation and experimental validation for human and mouse genomes',
......@@ -272,7 +272,7 @@ expert_dbs = [
],
'imported': True,
'status': 'updated',
'version': 'human 25/mouse M12',
'version': 'human 37/mouse M26',
},
{
'name': 'Rfam',
......@@ -502,7 +502,7 @@ expert_dbs = [
],
'imported': True,
'status': 'updated',
'version': '201', # ftp://ftp.ncbi.nlm.nih.gov/refseq/release/RELEASE_NUMBER
'version': '204', # ftp://ftp.ncbi.nlm.nih.gov/refseq/release/RELEASE_NUMBER
},
{
'name': 'RDP',
......@@ -551,7 +551,7 @@ expert_dbs = [
},
],
'imported': True,
'status': 'new',
'status': '',
'version': '',
},
{
......@@ -726,15 +726,28 @@ expert_dbs = [
},
{
'name': 'piRBase',
'label': '',
'label': 'pirbase',
'url': 'http://www.regulatoryrna.org/database/piRNA/',
'description': 'a web resource assisting piRNA functional study',
'hint': 'piRBase is a web resource assisting piRNA functional study',
'description': 'a database of various piRNA associated data to support piRNA functional study ',
'hint': 'piRBase is a database of various piRNA associated data to support piRNA functional study',
'tags': ['automatic', 'curated', 'piRNA'],
'abbreviation': '',
'examples': '',
'references': [],
'imported': False,
'examples': [
{'upi': 'URS0000061ED0', 'taxid': 9606},
{'upi': 'URS0000298B36', 'taxid': 10090},
{'upi': 'URS00000FDFAF', 'taxid': 7227},
],
'references': [
{
'title': 'piRBase: a comprehensive database of piRNA sequences',
'authors': 'Wang J, Zhang P, Lu Y, Li Y, Zheng Y, Kan Y, Chen R, He S',
'journal': 'Nucleic Acids Res. 2019 Jan 8;47(D1):D175-D180',
'pubmed_id': '30371818',
},
],
'imported': True,
'status': 'New',
'version': '2.0 (only sequences matching existing RNAcentral accessions have been imported)'
},
{
'name': 'PLncDB',
......@@ -917,7 +930,7 @@ expert_dbs = [
},
],
'imported': True,
'status': 'new',
'status': '',
'version': '',
},
{
......@@ -1379,7 +1392,7 @@ expert_dbs = [
},
],
'imported': True,
'status': 'new',
'status': 'updated',
'version': '',
},
{
......
......@@ -216,7 +216,7 @@ class Accession(models.Model):
'MALACARDS': 'https://www.genecards.org/cgi-bin/carddisp.pl?gene={id}#diseases',
'GENECARDS': 'https://www.genecards.org/cgi-bin/carddisp.pl?gene={id}',
}
if self.database in ['GTRNADB', 'ZWD', 'SNODB', 'MIRGENEDB', '5SRRNADB', 'SILVA', 'SNORNADB', 'ZFIN']:
if self.database in ['GTRNADB', 'ZWD', 'SNODB', 'MIRGENEDB', '5SRRNADB', 'SILVA', 'SNORNADB', 'ZFIN', 'PIRBASE']:
try:
data = json.loads(self.note)
url = data['url'] if 'url' in data else ''
......
......@@ -91,6 +91,12 @@
<a class="gtrnadb-external-url" ng-href="{{ xref.accession.expert_db_url }}" target="_blank">{{ xref.accession.optional_id }}</a>
</span>
<!-- piRBase -->
<span ng-switch-when="piRBase">
piRBase:
<a class="pirbase-external-url" ng-href="{{ xref.accession.expert_db_url }}" target="_blank">{{ xref.accession.external_id }}</a>
</span>
<!-- miRBase -->
<span ng-switch-when="miRBase">
miRBase:
......
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment