Difference between revisions of "Feature WishList"

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''This is a running list of proposed features at WormBase''
 
''This is a running list of proposed features at WormBase''
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== New displays, analysis, and data integration ==
  
 
===Human disease===
 
===Human disease===
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=== Micro/Macro Synteny; whole genome alignment===
 
=== Micro/Macro Synteny; whole genome alignment===
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== Tools ==
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=== Next-Gen Sequencing ===
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Revision as of 19:19, 5 October 2011

This is a running list of proposed features at WormBase

New displays, analysis, and data integration

Human disease

We need broader integration of human diseases. This is a benefit both to people who use C. elegans as a model system (most grants at least true to touch on the relevance of given projects with human disease) as well as those looking to the system to help understand orthologous genes implicated in disease.

Requirements:

  • should be possible to search by disease IDs and common names
  • genes with human orthologs implicated in disease should be clearly noted, probably in the Overview widget.
  • Should link back to OMIM

Status:

  • OMIM IDs in database; need brief descriptions?
  • Is there an OMIM web service we can consume?

Ontologies

We don't too much with ontology other than display a list of associations for a given object. What else can we do? For example, on the gene page, we could expand the ontology section to show genes with similar patterns of enrichment. We might also consider integrate a tool like AmiGO to make it easier to browse ontologies.

Suggestions:

  • show other genes with similar (aggregate) gene ontology

Homology/Orthology

We list homologs and orthologs of genes but provide no alignments. These should be readily available from the gene page.

Suggestions:

  • (pre-generate) alignments with orthologs via BLASTX
  • display in-line on the homology page or perhaps in lightbox
  • when available, overlay variations to help identify conserved and critical motifs

Variations

The ability to do forward genetics is one of the great strengths of C. elegans. We don't do enough with alleles identified in such screens. Can we gain additional information by looking at alleles in aggregate?

Suggestions:

  • Try to create an allelic series (organizing alleles from weakest to strongest) by looking at the type of allele (missense, nonsense, etc) and phenotype. Display on the gene page.
  • Null alleles are of particular interest. Call these out in listings with special formatting.
  • Map molecularly characterized variations against protein domains and cross reference with phenotypes to infer domain/protein function.

Natural variation

Micro/Macro Synteny; whole genome alignment

Tools

Next-Gen Sequencing

Back end

GBrowse consolidation

Currently we have GBrowse configuration in two places, as part of the website-gbrowse-support git repository and integrated into the new web app.

We need to maintain the website-gbrowse-support repository for the classic site. Going forward, I'd like to keep all config as a part of our app. For now, we need to make sure that any changes made to the classic site "website-gbrowse-support" repository also find their way into the configuration that is located in the new webapp.