Thank you Shraddha for your feedback, The external link is going to be reviewed. We agree that there are an inconvenient number of steps to actually locate the data on the external site to obtain the NCBI identifier, when available, for use in VisiGene and other tools/queries. This request will be prioritized along with our other projects, so I cannot comment on when/if this may be changed.
For your other comments, I will makes sure that these are forwarded to the development team for consideration when next discussing the data with the track collaborators. Your suggestions about how to make the data more understandable by the scientific community in the Methods description are valued. Thanks again for your input, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/21/10 6:33 PM, Shraddha Pai wrote: > Hi Jennifer, > Thanks for the detailed response! > > I did see the track description for the ABA track, and think it's > ambiguous. A colleague of mine first found it so, and so did I. I > suggest an additional sentence be added expressly stating that all > probes, regardless of brain-related expression, are included. > Alternately, there could be a sentence stating how probes were selected, > out of all the probes in the dataset. But either way, it needs to be > clear that a probe's presence on the track doesn't necessarily mean it > is expressed in brain tissue. > Would this be an addition made by someone at the ABI? > > It's a pity that there are a number of steps from identification of an > object on the ABA track and resolving it to an NCBI-related ID. > > Thanks for your help, > Shraddha > > > -----Original Message----- > From: Jennifer Jackson [mailto:[email protected]] > Sent: Wed 4/21/2010 8:57 PM > To: Shraddha Pai > Cc: [email protected] > Subject: Re: [Genome] Allen Brain track: what exactly does content mean? > > Hello Shraddha, > > The track description and following the data links from the track will > likely address most of these questions. Start by going into the mm8 > assembly and clicking on the track name "Allen Brain". > > Allen Brain Atlas Probes > Description > This track provides a link into the Allen Brain Atlas (ABA) images for > this probe. The ABA is an extensive database of high resolution in-situ > hybridization images of adult male mouse brains covering the majority of > genes. > > As stated, the track contains the probes. Expression information is > available from the data source. Click on a probe name to view the > detailed information for that data point and a link to the Allen Brain > Atlas: > http://www.brain-map.org/ > > Searching in mm8 with RP_050628_02_E04, and using the link from the > probe's detail page (click on probe name), the resulting Allen Brain > Atlas's web page is just the default page. > http://mouse.brain-map.org/search.do?queryText=egeneid=237360 > (this is not expected - I will run this by the development team) > > Since the search did not work correctly from the link, I did an > independent search with the term RP_050628_02_E04 using the upper right > search box to find: > http://www.brain-map.org/search/index.html?query=RP_050628_02_E04 > > Clicking into the resulting link finds: > http://mouse.brain-map.org/brain/gene/71489809.html > > Where the NCBI accession is noted as being: XM_137117 > > Using XM_137117 as a search term in UCSC's VisiGene finds one image with > the following annotation: > > source: Allen Brain Atlas (ABA) Reference: n/a > Year: 2006 Contributors: Boe A.,Dang C.,Jeung D.,Luong L.,Sunkin > S.,Sutram M.,Youngstrom B.,Lein E.,Jones A.,ABA ABA,ABI ABI,Allen > Institute for Brain Science,Allen Brain Atlas, > Gene: LOC237360 Probe: RNA sequenced GenBank: Organism: Mus musculus > Sex: male Strain: C57BL/6 Genotype: wild type > Stage: 5.3 week old pup (Theiler 28) Body Part: brain Expression: n/a > Section Type: sagittal > Copyright: © 2004-2006 Allen Institute for Brain Science > Acknowledgements: Thanks to the Allen Institute for Brain Science, > particularly to Andrew Boe, Chinh Dang, Darren Jeung, Lon Luong, Susan > Sunkin, Madhavi Sutram, and Brian Youngstrom for helping make these > images available in VisiGene.contributor Allen Institute for Brain Science > > Hopefully this is helpful. Thank you for asking your question since it > may have uncovered a problem link (likely something changed since the > track was first constructed). Very sorry for any confusion this may have > caused, > > Jennifer > > --------------------------------- > Jennifer Jackson > UCSC Genome Informatics Group > http://genome.ucsc.edu/ > > On 4/21/10 12:41 PM, Shraddha Pai wrote: > > Hi, > > > > I'm unclear as to what it means when a gene is shown in the Allen > Brain Atlas mouse track. > > Does it only mean that the probe was used for the FISH or does it > mean that the FISH did detect some non-zero level of expression in some > part of the mouse brain? > > > > (e.g. I'm looking at RP_050628_02_E04 in mouse build mm8 and am not > sure what that represents.) > > > > Moreover, when I enter this ID in the VisiGene search engine I don't > get any records in my result. > > > > Thanks in advance, > > Shraddha > > > > ______________________________________________________________________ > > This email has been scanned by the CAMH Email Security System. > > ______________________________________________________________________ > > _______________________________________________ > > Genome maillist - [email protected] > > https://lists.soe.ucsc.edu/mailman/listinfo/genome > > ______________________________________________________________________ > This email has been scanned by the CAMH Email Security System. > ______________________________________________________________________ > > > > ______________________________________________________________________ > This email has been scanned by the CAMH Email Security System. > ______________________________________________________________________ _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
