Hello, Anton, I don't know why the Table Browser output is tossing out the relationship between the individual items and their go.goaPart.aspect values. In the database they are separate:
mysql> SELECT * FROM goaPart WHERE dbObjectSymbol = "TAB2_RAT"; +------------+----------------+-------+------------+--------+ | dbObjectId | dbObjectSymbol | notId | goId | aspect | +------------+----------------+-------+------------+--------+ | Q5U303 | TAB2_RAT | | GO:0005622 | C | | Q5U303 | TAB2_RAT | | GO:0005634 | C | | Q5U303 | TAB2_RAT | | GO:0005737 | C | | Q5U303 | TAB2_RAT | | GO:0008270 | F | | Q5U303 | TAB2_RAT | | GO:0046872 | F | +------------+----------------+-------+------------+--------+ I see two ways to solve your problem. If you are technically capable of querying the database directly, you could use the public mysql server, genome-mysql. See this page for details: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29 Otherwise, you could apply a filter on the query and repeat it for each of the three aspect types (F,P,C). To do that: filter [create] Then you would follow the same table-intersection logic as before, to access the goaPart table via the relationship, rn4.rgdGene2 -> rn4.rgdGene2ToUniProt -> go.goaPart then set: aspect does match C (etc, in separate queries) this will give you separate output for each of the three aspect types. regards, --b0b kuhn ucsc genome bioinformatics group On 4/10/2012 9:11 PM, Anton Kratz wrote: > Hi Vanessa, > > thank you very much, this is almost what I was looking for, I have one > follow-up question though. I made a table following your instructions with > these fields: > > #rn4.rgdGene2.name go.goaPart.dbObjectId go.goaPart.dbObjectSymbol > go.goaPart.notId go.goaPart.goId go.goaPart.aspect > > Here is one example entry, for RGD:1309527 (Map3k7ip2): > > RGD:1309527 Q5U303, TAB2_RAT, , > GO:0005622,GO:0005634,GO:0005737,GO:0008270,GO:0046872, C,F, > > RGD:1309527 has five GO terms, two of them are Molecular Function > (GO:0008270,GO:0046872) and three of them are Cellular Component > (GO:0005622,GO:0005634,GO:0005737). But, from the table which I retrieve I > do not see how one can parse this information, because it just says "C,F" > it is unclear which GO terms are C and which ones are F. Shouldn't it be > something like "C,C,C,F,F"? Or maybe two tab-separated blocks splitting the > GO terms into C and F? > > I would like to ask how to get a table with all RGD genes (rn4 assembly) > and the associated Gene Ontology terms, in tab-separated ASCII, such that > it is still clear which GO term belongs to which of the three categories. > > Thank you very much, > Anton > > > On Tue, Apr 10, 2012 at 5:48 AM, Vanessa Kirkup Swing > <[email protected]>wrote: > >> Hi Anton, >> >> You will want to select the "rgdGene2ToUniProt" table. This will then give >> you the option at the top of the linked tables list to select "go.goaPart" >> which will then give you the option to select the individual fields from >> go.goaPart. >> >> If you have further questions or comments, please email the list: >> [email protected]. >> >> Vanessa Kirkup Swing >> UCSC Genome Bioinformatics Group >> >> >> ---------- Forwarded message ---------- >> From: Anton Kratz <[email protected]> >> Date: Thu, Apr 5, 2012 at 10:26 PM >> Subject: [Genome] RGD Genes and Gene Ontology for rn4 assembly via Table >> Browser >> To: UCSC Genome Browser Mailing List <[email protected]> >> >> >> Dear UCSC team, >> >> I would like to get a table with all RGD genes and the associated Gene >> Ontology terms, in tab-separated ASCII, for the rn4 assembly. >> >> I tried using the Table Browser for that, my idea was to start with the >> tack "RGD Genes" and the table "rgdGene2", then use "selected fields from >> primary and related tables" to find linked tables which will lead me to the >> GO terms. However, without success. >> >> Could you please explain how to get such a table? >> >> Thank you! >> >> Anton >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
