[ensembl-dev] Location of APPRIS and TSL in public mysql database for each Ensembl transcript

[Thibaut Hourlier]

Hi Alex,
You can find the data in the transcript_attrib table. You will need to join the attrib_type table too:
homo_sapiens_core_88_38 > SELECT t.stable_id, at.name, ta.value FROM transcript t, transcript_attrib ta, attrib_type at WHERE t.transcript_id = ta.transcript_id AND ta.attrib_type_id = at.attrib_type_id LIMIT 3;
+-----------------+--------------------------+-------------------+
| stable_id       | name                     | value             |
+-----------------+--------------------------+-------------------+
| ENST00000617849 | GENCODE basic annotation | GENCODE basic     |
| ENST00000617849 | Transcript Support Level | tsl1              |
| ENST00000466115 | Synonym                  | DAQB-124C11.3-007 |
+-----------------+--------------------------+—————————+

We would recommend you to use the Perl API to access this information if you need to do it often and in a safe way.
http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Transcript.html#a59f9ff2079a28ba80bc8b62a5e636327 <http://www.ensembl.org/info/docs/Doxygen/core-api/classBio_1_1EnsEMBL_1_1Transcript.html#a59f9ff2079a28ba80bc8b62a5e636327>

Thanks
Thibaut

> On 8 May 2017, at 06:48, Alexander Drew <a.drew at garvan.org.au> wrote:
> 
> Hello, 
> 
> I am trying to retrieve the flags (specifically APPRIS and Transcript support level) for Ensembl transcript Ids from the public mySQL database. I am having trouble locating this information in the database schema. I have found the reference for this in the various databases for the different genome builds, but cannot locate the actual data.
> 
> I am trying to grab the same data that is populated in the transcript table 'flags' column when viewing a gene in the Ensembl website (eg.http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000206195;r=22:15784959-15829984). <http://www.ensembl.org/Homo_sapiens/Gene/Summary?db=core;g=ENSG00000206195;r=22:15784959-15829984).>
> 
> can you help me find this data in the mySQL database?
> 
> Thank you,
> 
> Alex Drew.
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