Questions tagged [api]

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Running a list of apis via Python's request module

I am running the following Python code with python requests in my Jupiter notebook to get cancer oncology id's from EBI-EMBL. ...
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2 votes
0 answers
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How to retrieve Expression Atlas baseline expression results in JSON format?

I'm looking to retrieve Expression Atlas baseline expression results in JSON format, e.g. the results on this page. Several years ago I did a similar thing but looking at differential expression ...
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2 votes
1 answer
31 views

Taking too long to download metadata file (estimated size 30MB) from Covid-19 Data Portal

I am working on developing a tool to classify covid variants. So I am trying to download SARS-CoV-2 sequence data along with lineage annotation from Covid-19 Data Portal (I could not find a better ...
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0 votes
1 answer
15 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 ...
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1 vote
1 answer
26 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 ...
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2 votes
1 answer
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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%...
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2 votes
1 answer
37 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&...
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0 votes
1 answer
547 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 ...
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1 answer
109 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 ...
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  • 175
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1 answer
75 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 ...
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2 votes
0 answers
42 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 ...
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1 vote
1 answer
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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 ...
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0 votes
1 answer
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?
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1 vote
0 answers
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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.
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2 votes
0 answers
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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 ...
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5 votes
4 answers
239 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 ...
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  • 1,347
2 votes
1 answer
86 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 ...
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  • 325
1 vote
0 answers
181 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 ...
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3 votes
1 answer
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 ...
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  • 2,960
4 votes
2 answers
578 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 ...
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5 votes
3 answers
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 ...
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  • 757
14 votes
6 answers
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 ...
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  • 243
3 votes
2 answers
149 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 ...
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  • 1,012
7 votes
2 answers
209 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 ...
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13 votes
4 answers
548 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. ...
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