User: me
me • 680
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- @jervenbolleman
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Posts by me
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... We are at SIB Swiss-Prot working on UniProt are offsite, wait until thursday ;) ...
written 12 weeks ago by
me • 680
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... By chemistry is a bit limited so I need my colleague to help with stoichiometric factors and it's production week so time is hard to get. ...
written 3 months ago by
me • 680
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... Running out of space for the Rhea part, we will make a separate Q&A ...
written 3 months ago by
me • 680
2
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... 1) Is correct in the query with
?protein up:reviewed true .
2) The query in the Q. does not return anything for taxon:3702 as there are no rdfs:subClasses for Aribidopsis Thaliana, it is a leaf node. This means the entry is directly linked to that taxon instead of via it's ancestors. This i ...
written 3 months ago by
me • 680
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... It would probably work ok on our endpoint. But I think we got just the tool [you want, namely prosite][1]. I would also have a look at not using a database at all in that case as they will not perform optimally for your use case.
[1]: https://prosite.expasy.org/scanprosite/ ...
written 7 months ago by
me • 680
2
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... This is a comment because it is not at all answering your question. Instead of building your own database why not use our SPARQL.uniprot.org. This is likely to be better modelled than biosql is for the UniProt datamodel.
Otherwise I suspect your hardware is not at the level that one would use for ...
written 7 months ago by
me • 680
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... There are two issues with this query. The first is that in the PREFIX declaration there is an s missing at the end of proteome
i.e.
PREFIX proteome:
should be
PREFIX proteome:
The second one is more frustrating and is that the character '#' used in the fragment IRI is also seen as the ...
written 7 months ago by
me • 680
0
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... [pir peptide search][1] could be helpful even if it does not answer your question.
[1]: https://research.bioinformatics.udel.edu/peptidematch/commandlinetool.jsp ...
written 9 months ago by
me • 680
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Comment:
C: UniProt ID mapping API call
... Well they would be in a significant part be me ;) You can use the upload list facility on www.uniprot.org as well. Then you can use what ever columns you want. The real difficulty is actually with gene names and how they map to/from UniProt entries. The solutions to that are ask for exactly what you ...
written 10 months ago by
me • 680
0
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Comment:
C: UniProt ID mapping API call
... if you want the species/ncbi taxid just add a line "?protein up:organism ?taxon ." at the end of the where clause and "?taxon" on the select line. ...
written 10 months ago by
me • 680
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