User: me
me • 680
- Reputation:
- 680
- Status:
- Trusted
- Location:
- Switzerland
- Twitter:
- @jervenbolleman
- Last seen:
- 10 hours ago
- Joined:
- 4 years, 2 months ago
- Email:
- m*@jerven.eu
Posts by me
<prev
• 60 results •
page 1 of 6 •
next >
0
votes
1
answer
144
views
1
answers
... 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 8 days ago by
me • 680
0
votes
1
answer
144
views
1
answers
... Running out of space for the Rhea part, we will make a separate Q&A ...
written 14 days ago by
me • 680
2
votes
1
answer
144
views
1
answers
... 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 14 days ago by
me • 680
0
votes
1
answer
324
views
1
answers
... 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 4 months ago by
me • 680
2
votes
1
answer
324
views
1
answers
... 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 4 months ago by
me • 680
1
vote
1
answer
260
views
1
answers
... 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 4 months ago by
me • 680
0
votes
1
answer
369
views
1
answers
... [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 6 months ago by
me • 680
0
votes
2
answers
566
views
2
answers
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 7 months ago by
me • 680
0
votes
2
answers
566
views
2
answers
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 7 months ago by
me • 680
2
votes
2
answers
566
views
2
answers
Answer:
A: UniProt ID mapping API call
... You can use requests like
http://www.uniprot.org/uniprot/?query=accession:P13368&format=tab&columns=genes
to access only the gene names. However, the delimiting is a bit odd to parse in this case. i.e. some entries are linked to more than one gene. And genes often have more than one na ...
written 7 months ago by
me • 680
Latest awards to me
Scholar
14 days ago,
created an answer that has been accepted.
For A: Does UniProt have complete SNP information (from dbSNP)?
Popular Question
20 days ago,
created a question with more than 1,000 views.
For Image analysis specialist / scientific programmer | sciCORE University of Basel
Popular Question
3 months ago,
created a question with more than 1,000 views.
For Image analysis specialist / scientific programmer | sciCORE University of Basel
Teacher
4 months ago,
created an answer with at least 3 up-votes.
For A: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Appreciated
6 months ago,
created a post with more than 5 votes.
For A: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Good Answer
6 months ago,
created an answer that was upvoted at least 5 times.
For A: Downloading dataset of PTM sites from UniProt
Teacher
6 months ago,
created an answer with at least 3 up-votes.
For A: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Scholar
7 months ago,
created an answer that has been accepted.
For A: Does UniProt have complete SNP information (from dbSNP)?
Teacher
7 months ago,
created an answer with at least 3 up-votes.
For A: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Teacher
8 months ago,
created an answer with at least 3 up-votes.
For A: Get MW of a protein given a uniprot ID in R
Teacher
12 months ago,
created an answer with at least 3 up-votes.
For A: Get MW of a protein given a uniprot ID in R
Commentator
16 months ago,
created a comment with at least 3 up-votes.
For C: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Scholar
19 months ago,
created an answer that has been accepted.
For A: Get MW of a protein given a uniprot ID in R
Teacher
19 months ago,
created an answer with at least 3 up-votes.
For A: Get MW of a protein given a uniprot ID in R
Supporter
19 months ago,
voted at least 25 times.
Teacher
20 months ago,
created an answer with at least 3 up-votes.
For A: Get MW of a protein given a uniprot ID in R
Appreciated
3.6 years ago,
created a post with more than 5 votes.
For A: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Commentator
3.6 years ago,
created a comment with at least 3 up-votes.
For C: Genomics is not Special. Computational Biologist are reinventing the wheel for b
Teacher
3.6 years ago,
created an answer with at least 3 up-votes.
For A: Get MW of a protein given a uniprot ID in R
Scholar
3.6 years ago,
created an answer that has been accepted.
For A: Get MW of a protein given a uniprot ID in R
Scholar
3.7 years ago,
created an answer that has been accepted.
For A: Get MW of a protein given a uniprot ID in R
Scholar
3.8 years ago,
created an answer that has been accepted.
For A: Get MW of a protein given a uniprot ID in R
Teacher
3.8 years ago,
created an answer with at least 3 up-votes.
For A: Get MW of a protein given a uniprot ID in R
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1005 users visited in the last hour