Questions tagged [api]
The api tag has no usage guidance.
22
questions
0
votes
1answer
14 views
Getting all variants in a region from ensembl
I want to get all the variants (SNPs) in a given region of the human genome. Is there a way on how to do this with the ensembl-API? It should be a representation similar to this:
There I added dbSNP ...
1
vote
1answer
23 views
querying gdc metadata issues with resulting fields
I have been trying to access metadata from the Genomic Data Commons; however, not all of the information I want is showing up in the resulting tsv file. How do I get sample type and analyte type to ...
2
votes
1answer
42 views
How to extract all peptide sequences for a UniProt protein entry with an API?
I know how to generally pull down information for a UniProt entry using the REST API, for example:
https://www.uniprot.org/uniprot/?query=id:Q9UJL9&sort=score&columns=id,go(molecular%...
2
votes
1answer
34 views
Why is the UniProt REST API returning multiple results, when I am only providing one ID to be checked?
Can some explain why when I run a REST API query on UniProt for one ID ('Q9UJL9'), the results for three IDs are returned?
The query I'm using is:
https://www.uniprot.org/uniprot/?query=Q9UJL9&...
0
votes
1answer
374 views
OpenAPI-Generator Python Client Instructions Examples
Trying to learn a little bit of Python and Biopython I ended up figuring out what a Rest API is when the RCSB PDB repository released its new Rest API.
I tried to retrieve info from the PDB repository ...
1
vote
1answer
105 views
RCSB API: limited returned result
Is there a limit of query results on RCSB API?
Interestingly, no matter how to adjust my query criteria, only 10 assemblies are returned. Here is an example query json: (truncated from a longer query ...
0
votes
1answer
47 views
e-utils api: get chromosome position for each snp on a gene
So I have the following e-utils api-link:
https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=gene&db=snp&id=5726&retmode=json
it returns all the SNP-ids for the gene with ...
2
votes
0answers
39 views
Get nucleic acids' chain names from PDB API
There is a place in my pipeline where I call PDB's API with a ribosomal id to get all the subchains of that molecule programmatically
I'd like to separate subchains that are proteins from nucleic ...
1
vote
1answer
43 views
Getting species from ensembl sequence id
I have downloaded some orthologues from ensembl website in fasta format. The problem is that it uses the ensembl sequence id as name for the sequences. I want to know the species name or any other ...
0
votes
1answer
19 views
How to upload and process a data set to Galaxy instance and retrieve results programmatically?
How to upload and process (de novo assembly pipe) a data set to Galaxy instance and retrieve the results programmatically? Are there any packages beyond BioBlend?
1
vote
0answers
14 views
How to download all reactions of the TCA cycle from the RHEA database with the SPARQL endpoint?
I am looking for a way to use the SPARQL endpoint of RHEA to download all reactions of the TCA cycle in CSV or JSON format.
2
votes
0answers
58 views
Number of reactions per metabolic pathway
What is the quickest way to calculate the number of chemical reactions present in each pathway for a given organism and which online database such as Kegg, MetaCyc,Reactome is more helpful/reliable ...
5
votes
4answers
225 views
How do you query and explore ENCODE data?
I am looking for a modular way to query data from ENCODE.
For example, I would like to get CHiP-seq or similar tracks for a specific cell line. What's the proper way to do it?
Finally, is there an ...
2
votes
1answer
84 views
Error while performing "lift-over" of genomic coordinates between two species using Ensembl Compara API
I'm trying to convert coordinates between the reference mouse genome and CAST/EiJ mice strain. Since Ensebml already has alignment available in the browser, I decided to use Ensembl perl API to lift ...
1
vote
0answers
161 views
Multiple files for case in GDC data portal
I am downloading a set of Copy Number Variation samples from the GDC data API. I noticed that some cases have multiple files (aliquots) for the same case (see for example this case --- here the set of ...
3
votes
1answer
56 views
Automating sequence download from Wormbase
I'm working on the C. elegans model organism, for which there exists an online biological information database: Wormbase.
I'm able to manually search for a transcript (say "K06C4.12") and this gets ...
4
votes
2answers
531 views
Retrieve abstract/summary for NCBI bookshelf via Entrez
I want to retrieve abstracts/summaries for NCBI bookshelf entries, eg: "NBK1440"
Docs say the dbname is "books" and efetch guide says a rettype of "docsum" works for all databases. However when I ...
5
votes
3answers
2k views
How to map PDB chains to Uniprot IDs using API services
I have a lot of PDB IDs and I need to get uniprot fasta sequences of these PDB IDs special chains by API services. For example, imagine that I need to get fasta sequence of '1kf6' 'A' chain. The ...
13
votes
6answers
2k views
Is there public RESTful api for Gnomad?
I currently find Harvard's RESTful API for ExAC extremely useful and I was hoping that a similar resource is available for Gnomad?
Does anyone know of a public access API for Gnomad or possibly any ...
3
votes
2answers
148 views
How can I find mutations associated with disease in human histone residues?
I would like to look if there are mutations in residues of human histones associated with any disease. For instance, if a mutation in residue K6 (lysine 6) of histone H2A1A is associated with any ...
7
votes
2answers
195 views
What methods should I use from PythonCyc API to query metabolites in BioCyc database?
I am using PythonCyc API in order to write a query for metabolites in BioCyc. The purpose of this API is to communicate with the database software of BioCyc- Pathway Tools. Pathway Tools is in lisp ...
13
votes
4answers
531 views
Library for computing BWT-based alignments
I am writing a software tool to which I would like to add the ability to compute alignments using the efficient Burrows-Wheeler Transform (BWT) approach made popular by tools such as BWA and Bowtie. ...
