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1answer
82 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
0answers
12 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 ...
1
vote
0answers
23 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 ...
0
votes
0answers
11 views

Finding associated diseases of my collection of diseases extracted from DisGeNET

Goal: I have 101 diseases. (extract from DisGeNET) I want to get associated diseases of these 101 diseases. to validated disease graph that I created. Note: Associated could be measured by jaccard ...
1
vote
1answer
28 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
18 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
12 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
48 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
173 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
67 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
94 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
51 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
358 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
1k 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
4answers
1k 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
144 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
165 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 ...
11
votes
4answers
451 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. ...