Bioinformatics Discussion Group

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(Construction of web based query pages that can access multiple databases)
 
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*With regards to Gene Ontology, check out the [http://dimer.tamu.edu/GO/wiki GO wiki] put out by Jim Hu at UT Austin.  It's just starting up, but you may want to talk to him to get more information. --[[User:Skosuri|Sri Kosuri]] 15:40, 7 Nov 2005 (EST)
*With regards to Gene Ontology, check out the [http://dimer.tamu.edu/GO/wiki GO wiki] put out by Jim Hu at UT Austin.  It's just starting up, but you may want to talk to him to get more information. --[[User:Skosuri|Sri Kosuri]] 15:40, 7 Nov 2005 (EST)
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*While coordinating links and orthologs would be useful, what I find most lacking in the current databases is the lack of a reasonable expert summary of the major known roles of the protein and key references.  I find it difficult to rapidly get my bearings about the functions of a particular list of regulated genes, for example.  I've been thinking that a wiki-based gene encyclopedia format which could hold user-entered information on each gene would be a more dynamic and useful resource. It could also house links to other databases and list orthologs. --[[User:StuartSealfon|Stuart Sealfon]]  29 December 2005
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*You also have to be careful in your assertions: BLAST will not find orthologs and paralogs, but rather BLAST will find similar sequences, from which you can declare that certain members of that list are orthologs or paralogs. That later statement being a scientific interpretation of the BLAST experiment you will have done. [[User:Francis|Francis Ouellette]] 02:07, 4 March 2006 (EST)
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* That said, I'm not sure this is the right media for this sort of discussion, but rather maybe a place to put links to resource we think are useful for bioinformatics, or links to places where orthologs and paralogs are appropriatly defined! [[User:Francis|Francis Ouellette]] 02:07, 4 March 2006 (EST)
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* Accessing multiple databases???? Why not simply go to [http://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi?term=all+%5Bfilter%5D NCBI]? [[User:Francis|Francis]] 02:11, 4 March 2006 (EST)
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==Computational Tools/Machines/Devices for Biology Protocols==
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* Added [[Computing/Robotics]] for Tecan, BioMek, etc, which hasnt been created here yet.  I would also like to see software engineering hosted on OWW, for example "java applet to control our [whatever] equipment"  --'''[[User:Jonathan Cline|jcline@ieee.org]] 17:36, 29 July 2009 (EDT)'''

Current revision

I am curious to know if Openwetware can be used to discuss bioinformatics. In particular, the field of bioinformatics is maturing as more scientists become familiar with the various tools that are available via the Internet. However, this might be a good time to share ideas, either general or specific, about future needs in this field. To start this off, it seemed reasonable to me that I would mention an area that might benefit from further development:

Construction of web based query pages that can access multiple databases

As a biologist, I frequently would like to collect information about orthologs and paralogs in multiple species, as this frequently will help me formulate hypotheses. Of course, I realize that BLAST is an invaluable tool, but I frequently need to reach beyond NCBI entries to various model organism databases. One useful approach might be a web interface that is 'gene centric' and would allow me to select various target databases (MODs, NCBI, ENSEMBL etc.) for the input query. Perhaps the program could start with BLAST and identify orthologs and paralogs in various species of interest. I might also want the program to collect Gene Ontology terms from appropriate databases providing some insight into either known or predicted function. Finally, the program would launch a HUBMED search and collect references regarding the gene products. Finally, perhaps the results could be saved to a web page with hot links to the collected information.

The question I have is: Do you think such a resource would be valuable? If so, what other sort of information might you like to collect? What other applications would be useful for development?

  • With regards to Gene Ontology, check out the GO wiki put out by Jim Hu at UT Austin. It's just starting up, but you may want to talk to him to get more information. --Sri Kosuri 15:40, 7 Nov 2005 (EST)
  • While coordinating links and orthologs would be useful, what I find most lacking in the current databases is the lack of a reasonable expert summary of the major known roles of the protein and key references. I find it difficult to rapidly get my bearings about the functions of a particular list of regulated genes, for example. I've been thinking that a wiki-based gene encyclopedia format which could hold user-entered information on each gene would be a more dynamic and useful resource. It could also house links to other databases and list orthologs. --Stuart Sealfon 29 December 2005
  • You also have to be careful in your assertions: BLAST will not find orthologs and paralogs, but rather BLAST will find similar sequences, from which you can declare that certain members of that list are orthologs or paralogs. That later statement being a scientific interpretation of the BLAST experiment you will have done. Francis Ouellette 02:07, 4 March 2006 (EST)
  • That said, I'm not sure this is the right media for this sort of discussion, but rather maybe a place to put links to resource we think are useful for bioinformatics, or links to places where orthologs and paralogs are appropriatly defined! Francis Ouellette 02:07, 4 March 2006 (EST)
  • Accessing multiple databases???? Why not simply go to NCBI? Francis 02:11, 4 March 2006 (EST)


Computational Tools/Machines/Devices for Biology Protocols

  • Added Computing/Robotics for Tecan, BioMek, etc, which hasnt been created here yet. I would also like to see software engineering hosted on OWW, for example "java applet to control our [whatever] equipment" --jcline@ieee.org 17:36, 29 July 2009 (EDT)
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