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  1. IGB 8.1
  2. IGBE-26

Test weblinks

          Details

          • Type: Task
          • Status: Reopened (View Workflow)
          • Priority: Minor
          • Resolution: Unresolved
          • Labels:
            None

            Description

            Test weblinks for all version present in our quickload i.e. http://igbquickload.org/quickload/

            Plants from Phytozome should provide successful links to phytozome. A thal should have links to TAIR. Animals should have links (for EST and mRNA files) to NCBI. All files should have a link to google.

            Marc 2014 update:

            There should no longer be any links to Phytozome or Metazome. These were too difficult to maintain. All tracks named EST or mRNA should link to NCBI, also.

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                relates to

                Task - A task that needs to be done. BUG-674 Weblinks

                • Blocker - Blocks development and/or testing work, production could not run.
                • Closed

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                  hiralv Hiral Vora (Inactive) created issue -
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                  ann.loraine Ann Loraine added a comment -

                  The maizegenome.org link works okay. I haven't tested the Phytozome links because the site appears to be down at the moment.

                  Show
                  ann.loraine Ann Loraine added a comment - The maizegenome.org link works okay. I haven't tested the Phytozome links because the site appears to be down at the moment.
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                  ann.loraine Ann Loraine added a comment -

                  OK. I tested the Phytozome links. They worked fine.

                  Show
                  ann.loraine Ann Loraine added a comment - OK. I tested the Phytozome links. They worked fine.
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                  ann.loraine Ann Loraine added a comment -

                  I have tested the new link patterns with A lyrata, B distachyon, and the March 2010 and 2009 Maize genomes. They are working fine.

                  Show
                  ann.loraine Ann Loraine added a comment - I have tested the new link patterns with A lyrata, B distachyon, and the March 2010 and 2009 Maize genomes. They are working fine.
                  ann.loraine Ann Loraine made changes -
                  Field Original Value New Value
                  Status Open [ 1 ] Resolved [ 5 ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Resolved [ 5 ] Reopened [ 4 ]
                  Assignee Alyssa Gulledge [ alyssa ] Katharine Kubiak [ kkubiak ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Project IGB6.6 [ 10021 ] Bug Repository [ 10030 ]
                  Key IGBA-231 BUG-225
                  Hide
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                  kkubiak Katharine Kubiak (Inactive) added a comment -

                  Passed v9824 Windows

                  Show
                  kkubiak Katharine Kubiak (Inactive) added a comment - Passed v9824 Windows
                  kkubiak Katharine Kubiak (Inactive) made changes -
                  Assignee Katharine Kubiak [ kkubiak ] Anuj Puram [ anuj ]
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                  anuj Anuj Puram (Inactive) added a comment -

                  Passed 6.7.0 (9891) on Mac

                  Show
                  anuj Anuj Puram (Inactive) added a comment - Passed 6.7.0 (9891) on Mac
                  anuj Anuj Puram (Inactive) made changes -
                  Assignee Anuj Puram [ anuj ] Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Resolved [ 5 ] Closed [ 6 ]
                  fwang4 Fuquan Wang (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Closed [ 6 ] Reopened [ 4 ]
                  Assignee Fuquan Wang [ fwang4 ]
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                  fwang4 Fuquan Wang (Inactive) added a comment - - edited

                  Passed for 7.0.0 (11982) Mac

                  Show
                  fwang4 Fuquan Wang (Inactive) added a comment - - edited Passed for 7.0.0 (11982) Mac
                  fwang4 Fuquan Wang (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Fuquan Wang [ fwang4 ]
                  Resolution Fixed [ 1 ]
                  richard Richard Linchangco (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Resolved [ 5 ] Reopened [ 4 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue relates to BUG-623 [ BUG-623 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue relates to BUG-623 [ BUG-623 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Link This issue relates to BUG-674 [ BUG-674 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Description Test weblinks for all version present in our quickload i.e. http://igbquickload.org/quickload/

                  Make sure that you use your clear script to clear igb first. You can latest revision of igb 6.6 from here http://test.bioviz.org/igb_release/                   		Test weblinks for all version present in our quickload i.e. http://igbquickload.org/quickload/

                  Plants from Phytozome should provide successful links to phytozome. A thal should have links to TAIR. Animals should have links (for EST and mRNA files) to NCBI. All files should have a link to google.
                  Hide
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                  richard Richard Linchangco (Inactive) added a comment -

                  Currently testing ALL links associated with Gene Models, mRNA models, and ESTs

                  Show
                  richard Richard Linchangco (Inactive) added a comment - Currently testing ALL links associated with Gene Models, mRNA models, and ESTs
                  Hide
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                  richard Richard Linchangco (Inactive) added a comment -

                  Ailuropoda melanoleuca Dec 2009

                  • EnsGene
                    • Links out to Google

                  Anolis carolinensis May 2010

                  • ensGene
                    • Link to UCSC Browser
                    • Google

                  Anopheles gambiae Feb 2003

                  • EnsGene
                    • Links out to Google
                  • mRNA
                    • Google
                    • NCBI
                  • EST
                    • Google
                    • NCBI

                  Apis mellifera Jan 2005

                  • RefGene
                    • Google-Doesn't find anything
                      • Ex: AmeLGUn_WGA742_2.501998.501998.m (TOO specific of a name)
                    • NCBI-Doesn't find anything
                      • Ex: AmeLGUn_WGA742_2.501998.501998.m (TOO specific of a name)
                  • mRNA
                    • Google
                    • NCBI
                  • EST
                    • Google
                    • NCBI

                  Aplysia californica Sep 2008

                  • NO REFERENCE

                  Arabidopsis lyrata Apr 2011

                  • Phytozome v7
                    • Google
                    • Phytozome

                  Arabidopsis thaliana Jun 2009

                  • TAIR10 mRNA
                    • Google
                    • TAIR
                  • TDNA insertion lines
                    • Google

                  A. thaliana 2008

                  • TAIR8 mRNA
                    • Google
                    • TAIR
                  • TAIR8 tRNA
                    • Google
                    • TAIR
                  • TAIR8 miRNA
                    • Google
                    • TAIR
                  • TAIR8 ncRNA
                    • Google
                    • TAIR
                  • TAIR8 snRNA
                    • Google
                    • TAIR
                  • TAIR8 snoRNA
                    • Google
                    • NCBI
                  • TAIR8 rRNA
                    • NO READS

                  A. thaliana 2004

                  • Protein-coding
                    • Google
                    • TAIR
                  • TAIR7 miRNA
                    • Google
                    • NCBI
                  • TAIR7 rRNA
                    • NO READS
                  • TAIR7 tRNA
                    • Google
                    • TAIR
                  • TAIR7 other RNA
                    • Google
                    • TAIR
                  • TAIR7 snoRNA
                    • Google
                    • TAIR
                  • TAIR7 pseudogenes
                    • Google
                    • TAIR
                  • TAIR7 snRNAs
                    • Google
                    • TAIR

                  Bos taurus Oct 2011

                  • RefGene
                    • Google
                    • NCBI
                  • mRNA
                    • Google
                    • NCBI
                  • EST
                    • Google
                    • NCBI

                  B. taurus 2009

                  • refGene
                    • Link to UCSC Browser
                    • Google
                    • NCBI

                  B. taurus 2007

                  • genscan
                    • Google
                  • mgcGenes
                    • Google
                  • mRNA
                    • Google
                    • NCBI
                  • refseq
                    • Google
                    • NCBI

                  B. taurus 2006

                  • refGene
                    • Link to UCSC Browser
                    • Google
                    • NCBI

                  B. taurus 2005

                  • refGene
                    • Link to UCSC Browser
                    • Google
                    • NCBI

                  STILL TESTING LINKS, UPDATE

                  Show
                  richard Richard Linchangco (Inactive) added a comment - Ailuropoda melanoleuca Dec 2009 EnsGene Links out to Google Anolis carolinensis May 2010 ensGene Link to UCSC Browser Google Anopheles gambiae Feb 2003 EnsGene Links out to Google mRNA Google NCBI EST Google NCBI Apis mellifera Jan 2005 RefGene Google-Doesn't find anything Ex: AmeLGUn_WGA742_2.501998.501998.m (TOO specific of a name) NCBI-Doesn't find anything Ex: AmeLGUn_WGA742_2.501998.501998.m (TOO specific of a name) mRNA Google NCBI EST Google NCBI Aplysia californica Sep 2008 NO REFERENCE Arabidopsis lyrata Apr 2011 Phytozome v7 Google Phytozome Arabidopsis thaliana Jun 2009 TAIR10 mRNA Google TAIR TDNA insertion lines Google A. thaliana 2008 TAIR8 mRNA Google TAIR TAIR8 tRNA Google TAIR TAIR8 miRNA Google TAIR TAIR8 ncRNA Google TAIR TAIR8 snRNA Google TAIR TAIR8 snoRNA Google NCBI TAIR8 rRNA NO READS A. thaliana 2004 Protein-coding Google TAIR TAIR7 miRNA Google NCBI TAIR7 rRNA NO READS TAIR7 tRNA Google TAIR TAIR7 other RNA Google TAIR TAIR7 snoRNA Google TAIR TAIR7 pseudogenes Google TAIR TAIR7 snRNAs Google TAIR Bos taurus Oct 2011 RefGene Google NCBI mRNA Google NCBI EST Google NCBI B. taurus 2009 refGene Link to UCSC Browser Google NCBI B. taurus 2007 genscan Google mgcGenes Google mRNA Google NCBI refseq Google NCBI B. taurus 2006 refGene Link to UCSC Browser Google NCBI B. taurus 2005 refGene Link to UCSC Browser Google NCBI STILL TESTING LINKS, UPDATE
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                  richard Richard Linchangco (Inactive) added a comment -

                  Continued Testing:
                  Let it be noted that from here only missing species will be listed (although ALL up to the last listed has been tested).
                  Many link to proper Google pages but are unable to return search results, resultant of the length of the query. These are not listed but a record file can be produced from my computer.
                  NCBI links that are incorrect ARE listed below.

                  Caenorhabditis briggsae Jan 2007

                  • xenoRefGene
                    • Link to UCSC Browser
                    • Google-Doesn't find anything
                      • Ex: NM_025451.chrI.2513370 (too specific)
                  • est
                    • Link to UCSC Browser
                    • Google-Doesn't find anything
                      • Ex: R04550.chrI.2601350 (too specific)
                    • NCBI-Page NOT found
                  • mrna
                    • Link to UCSC Browser
                    • Google-Doesn't find anything
                      • Ex: AY589606.chrI.4693224 (too specific)
                    • NCBI-Page not found

                  C. elegans 2008

                  • RefSeq Genes
                    • Google
                    • SHOULD HAVE NCBI LINK
                  • WormBase Genes
                    • Google
                    • SHOULD HAVE WORMBASE LINK
                  • WormBase PseudoGenes
                    • Google
                    • SHOULD HAVE WORMBASE LINK

                  C. elegans 2007

                  • RefSeq Genes
                    • Link to UCSC Browser
                    • Google
                    • NCBI-Page NOT found
                  • mrna
                    • Link to UCSC Browser
                    • Google
                    • NCBI-Page NOT found
                  • est
                    • Link to UCSC Browser
                    • Google-Doesn't find anything
                      • Ex: C59050.chrI.4015239 (too specific)
                    • NCBI-Page NOT found

                  C. elegans 2004

                  • refGene
                    • Link to UCSC Browser
                    • Google-Doesn't find anything
                      • Ex: FN876302.chrI.19195
                    • NCBI-Page NOT found
                  • mrna
                    • Link to UCSC Browser
                    • Google
                    • NCBI-Page NOT found
                  • est
                    • Link to UCSC Browser
                    • Google-Doesn't find anything
                      • Ex: FN871719.chrI.30140
                    • NCBI-Page NOT found

                  Candida albicans SC5314 Assembly 21

                  • Gene models (candidagenome.org)
                    • Google
                    • SHOULD HAVE LINK OUT TO candidagenome.org PAGE

                  Candida albicans WO-1 Jul 2010

                  • NO REFERENCES

                  Dictyostelium discoideum May 2009

                  • Curated genes (July 2010)
                    • DictyBase
                    • Google
                  • ALL
                    • DictyBase
                    • Google
                  • Gene predictions
                    • DictyBase
                    • Google
                  • Geneid re-predictions
                    • NO DATA
                  • tRNAs from tRNAscan-SE
                    • DictyBase
                    • Google
                  • ncRNAs
                    • DictyBase
                    • Google
                  • ncRNAs (Genbank)
                    • NO DATA
                  Show
                  richard Richard Linchangco (Inactive) added a comment - Continued Testing: Let it be noted that from here only missing species will be listed (although ALL up to the last listed has been tested). Many link to proper Google pages but are unable to return search results, resultant of the length of the query. These are not listed but a record file can be produced from my computer. NCBI links that are incorrect ARE listed below. Caenorhabditis briggsae Jan 2007 xenoRefGene Link to UCSC Browser Google-Doesn't find anything Ex: NM_025451.chrI.2513370 (too specific) est Link to UCSC Browser Google-Doesn't find anything Ex: R04550.chrI.2601350 (too specific) NCBI-Page NOT found mrna Link to UCSC Browser Google-Doesn't find anything Ex: AY589606.chrI.4693224 (too specific) NCBI-Page not found C. elegans 2008 RefSeq Genes Google SHOULD HAVE NCBI LINK WormBase Genes Google SHOULD HAVE WORMBASE LINK WormBase PseudoGenes Google SHOULD HAVE WORMBASE LINK C. elegans 2007 RefSeq Genes Link to UCSC Browser Google NCBI-Page NOT found mrna Link to UCSC Browser Google NCBI-Page NOT found est Link to UCSC Browser Google-Doesn't find anything Ex: C59050.chrI.4015239 (too specific) NCBI-Page NOT found C. elegans 2004 refGene Link to UCSC Browser Google-Doesn't find anything Ex: FN876302.chrI.19195 NCBI-Page NOT found mrna Link to UCSC Browser Google NCBI-Page NOT found est Link to UCSC Browser Google-Doesn't find anything Ex: FN871719.chrI.30140 NCBI-Page NOT found Candida albicans SC5314 Assembly 21 Gene models (candidagenome.org) Google SHOULD HAVE LINK OUT TO candidagenome.org PAGE Candida albicans WO-1 Jul 2010 NO REFERENCES Dictyostelium discoideum May 2009 Curated genes (July 2010) DictyBase Google ALL DictyBase Google Gene predictions DictyBase Google Geneid re-predictions NO DATA tRNAs from tRNAscan-SE DictyBase Google ncRNAs DictyBase Google ncRNAs (Genbank) NO DATA
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                  richard Richard Linchangco (Inactive) added a comment -

                  Final section of testing for weblinks

                  Escherichia coli K12 MG1655 Jan 2012

                  • Genbank
                    • Google
                    • SHOULD HAVE LINK TO GENBANK

                  Loxodonta africana Jul 2009

                  • EnsGene
                    • Google
                    • SHOULD HAVE LINK TO ENSEMBLE

                  Oryza sativa japonica Oct 2011

                  • RGAP gene models
                    • Google
                    • SHOULD HAVE LINK TO RGAP source

                  O sativa japonica June 2009

                  • gene models from Phytozome v7
                    • Google
                    • Phytozome-Page is EMPTY

                  Populus trichocarpa Jan 2010

                  • gene models from Phytozome v7
                    • Google
                    • Phytozome-Page is EMPTY

                  Shcizosaccharomyces bombe May 2012

                  • Reference genes
                    • Google
                    • SHOULD HAVE LINK TO SOURCE OF reference genes

                  Solanum lycopersicum May 2012

                  • ITAG2.3
                    • Google
                    • SHOULD HAVE LINK TO SOURCE OF ITAG2.3

                  Thellungiella parvula May 2012

                  • FGenesh++
                    • Google
                    • SHOULD HAVE LINK OUT TO SOURCE of FGenesh++

                  Thermococcus kodakaraensis KOD1 May 2004

                  • gene
                    • Google
                    • SHOULD HAVE LINK TO SOURCE FROM gene

                  Volvox carteri Jul 2010

                  • gene models from Phytozome v7
                    • Google
                    • Phytozome-Page is EMPTY
                  Show
                  richard Richard Linchangco (Inactive) added a comment - Final section of testing for weblinks Escherichia coli K12 MG1655 Jan 2012 Genbank Google SHOULD HAVE LINK TO GENBANK Loxodonta africana Jul 2009 EnsGene Google SHOULD HAVE LINK TO ENSEMBLE Oryza sativa japonica Oct 2011 RGAP gene models Google SHOULD HAVE LINK TO RGAP source O sativa japonica June 2009 gene models from Phytozome v7 Google Phytozome-Page is EMPTY Populus trichocarpa Jan 2010 gene models from Phytozome v7 Google Phytozome-Page is EMPTY Shcizosaccharomyces bombe May 2012 Reference genes Google SHOULD HAVE LINK TO SOURCE OF reference genes Solanum lycopersicum May 2012 ITAG2.3 Google SHOULD HAVE LINK TO SOURCE OF ITAG2.3 Thellungiella parvula May 2012 FGenesh++ Google SHOULD HAVE LINK OUT TO SOURCE of FGenesh++ Thermococcus kodakaraensis KOD1 May 2004 gene Google SHOULD HAVE LINK TO SOURCE FROM gene Volvox carteri Jul 2010 gene models from Phytozome v7 Google Phytozome-Page is EMPTY
                  richard Richard Linchangco (Inactive) made changes -
                  Assignee Hiral Vora [ hiralv ]
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                  hiralv Hiral Vora (Inactive) added a comment -

                  Probably need new url. Do you know which url to use?

                  Show
                  hiralv Hiral Vora (Inactive) added a comment - Probably need new url. Do you know which url to use?
                  hiralv Hiral Vora (Inactive) made changes -
                  Assignee Hiral Vora [ hiralv ] Alyssa Gulledge [ alyssa ]
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                  alyssa Alyssa Gulledge (Inactive) added a comment - - edited

                  After back checking, these are the current weblink issues

                  needs to be fixed

                  P tricho... does NOT successfully link to phytozome
                  A mellifera does not successfully pull up NCBI link

                  Needs NCBI links:

                  T koda...
                  E coli

                  Needs specialized links:

                  T parvula: thullengiella.org
                  S lycop... : http://solgenomics.net/organism/Solanum_lycopersicum/genome
                  S pombe: http://www.pombase.org/
                  O sativa (2011): http://rice.plantbiology.msu.edu
                  C albicans: http://www.candidagenome.org

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - - edited After back checking, these are the current weblink issues needs to be fixed P tricho... does NOT successfully link to phytozome A mellifera does not successfully pull up NCBI link Needs NCBI links: T koda... E coli Needs specialized links: T parvula: thullengiella.org S lycop... : http://solgenomics.net/organism/Solanum_lycopersicum/genome S pombe: http://www.pombase.org/ O sativa (2011): http://rice.plantbiology.msu.edu C albicans: http://www.candidagenome.org
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ] Ann Loraine [ aloraine ]
                  hiralv Hiral Vora (Inactive) made changes -
                  Assignee Ann Loraine [ aloraine ] Alyssa Gulledge [ alyssa ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Status Reopened [ 4 ] Resolved [ 5 ]
                  Assignee Alyssa Gulledge [ alyssa ]
                  Resolution Fixed [ 1 ]
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                  alyssa Alyssa Gulledge (Inactive) added a comment -

                  The last bit is correct in that the specialized links, the missing phytozome links, etc. are all still missing. However, at this time, there is nothing broken.

                  Moving this into 8.1, because it should be fixed at some point.

                  Show
                  alyssa Alyssa Gulledge (Inactive) added a comment - The last bit is correct in that the specialized links, the missing phytozome links, etc. are all still missing. However, at this time, there is nothing broken . Moving this into 8.1, because it should be fixed at some point.
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Resolution Fixed [ 1 ]
                  Status Resolved [ 5 ] Reopened [ 4 ]
                  alyssa Alyssa Gulledge (Inactive) made changes -
                  Project Bug Repository [ 10030 ] IGB 8.1 [ 10640 ]
                  Key BUG-225 IGBE-26
                  Issue Type Task [ 3 ] Bug [ 1 ]
                  hiralv Hiral Vora (Inactive) made changes -
                  Assignee Tarun Santosh [ tkanapar ]
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                  tkanapar Tarun Santosh (Inactive) added a comment -

                  Passed v15841 Mac

                  Show
                  tkanapar Tarun Santosh (Inactive) added a comment - Passed v15841 Mac
                  tkanapar Tarun Santosh (Inactive) made changes -
                  Assignee Tarun Santosh [ tkanapar ] Alyssa Gulledge [ alyssa ]
                  hiralv Hiral Vora (Inactive) made changes -
                  Assignee Alyssa Gulledge [ alyssa ] Kyle Suttlemyre [ kyle ]
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                  kyle Kyle Suttlemyre (Inactive) added a comment -

                  Instead of updating/testing urls manually attempt to make google work for us for the phytozome links

                  create google links in the form of
                  http://www.google.com/search?&sourceid=navclient&btnI=I&q=site%3Aphytozome.net%20<ID>

                  What this url does is uses google to do a site specific search on phytozome.net for the specific <ID> and then do an "I'm feeling lucky" redirect to the top results

                  Resource:
                  http://webapps.stackexchange.com/questions/53554/googles-im-feeling-lucky-url

                  Show
                  kyle Kyle Suttlemyre (Inactive) added a comment - Instead of updating/testing urls manually attempt to make google work for us for the phytozome links create google links in the form of http://www.google.com/search?&sourceid=navclient&btnI=I&q=site%3Aphytozome.net%20 <ID> What this url does is uses google to do a site specific search on phytozome.net for the specific <ID> and then do an "I'm feeling lucky" redirect to the top results Resource: http://webapps.stackexchange.com/questions/53554/googles-im-feeling-lucky-url
                  ann.loraine Ann Loraine made changes -
                  Assignee Kyle Suttlemyre [ kyle ] Ann Loraine [ aloraine ]
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                  ann.loraine Ann Loraine added a comment -

                  Please test web links after Ann's pull request is added to development branch.

                  Show
                  ann.loraine Ann Loraine added a comment - Please test web links after Ann's pull request is added to development branch.
                  ann.loraine Ann Loraine made changes -
                  Assignee Ann Loraine [ aloraine ] Kyle Suttlemyre [ kyle ]
                  ann.loraine Ann Loraine made changes -
                  Issue Type Bug [ 1 ] Task [ 3 ]
                  Priority Major [ 3 ] Minor [ 4 ]
                  ann.loraine Ann Loraine made changes -
                  Description Test weblinks for all version present in our quickload i.e. http://igbquickload.org/quickload/

                  Plants from Phytozome should provide successful links to phytozome. A thal should have links to TAIR. Animals should have links (for EST and mRNA files) to NCBI. All files should have a link to google.                   		Test weblinks for all version present in our quickload i.e. http://igbquickload.org/quickload/

                  Plants from Phytozome should provide successful links to phytozome. A thal should have links to TAIR. Animals should have links (for EST and mRNA files) to NCBI. All files should have a link to google.

                  Marc 2014 update:

                  There should no longer be any links to Phytozome or Metazome. These were too difficult to maintain. All tracks named EST or mRNA should link to NCBI, also.
                  Hide
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                  ann.loraine Ann Loraine added a comment -

                  Only need to test linkouts from QuickLoad genome versions.
                  Any track with track name containing the string "mRNA" or "EST" should link out to NCBI.
                  Ex) http://www.ncbi.nlm.nih.gov/nuccore/HQ318070 is the linkout from an m
                  RNA record with id HQ318070.

                  Show
                  ann.loraine Ann Loraine added a comment - Only need to test linkouts from QuickLoad genome versions. Any track with track name containing the string "mRNA" or "EST" should link out to NCBI. Ex) http://www.ncbi.nlm.nih.gov/nuccore/HQ318070 is the linkout from an m RNA record with id HQ318070.
                  mason Mason Meyer (Inactive) made changes -
                  Assignee Kyle Suttlemyre [ kyle ] Mason Meyer [ mason ]
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                  mason Mason Meyer (Inactive) added a comment - - edited

                  *Recommendations from this testing for more accurate search results:
                  1) We should add the description and species to the Gene ID in the Google search.
                  2) We should convert underscores to spaces for Google search.

                  A_gambiae_Feb_2003/
                  -EnsGene:
                  Google
                  -mRNA:
                  Google
                  NCBI
                  -EST:
                  Google
                  NCBI

                  A_lyrata_Apr_2011/
                  -Phytozome v7:
                  Google (irrelevant search)

                  A_melanoleuca_Dec_2009/
                  -EnsGene:
                  Google
                  -mRNA:
                  Google
                  NCBI
                  -EST:
                  Google
                  NCBI

                  A_mellifera_Jan_2005/
                  -RefGene:
                  Google
                  *Ex: AmeLGUn_WGA742_2.501998.501998.m (from Richard Linchancgo's testing)
                  *The underscores should actually be converted to spaces for Google
                  NCBI (inconsistent behavior; several broken links)
                  -mRNA:
                  Google
                  NCBI
                  -EST:
                  Google
                  NCBI

                  A_thaliana_Apr_2008/
                  -TAIR8 mRNA:
                  Google
                  TAIR
                  -TAIR8 tRNA:
                  Google
                  TAIR
                  -TAIR8 miRNA:
                  Google
                  TAIR
                  -TAIR8 ncRNA:
                  Google
                  TAIR
                  -TAIR8 snRNA:
                  Google
                  TAIR
                  -TAIR8 snoRNA:
                  Google
                  TAIR
                  -TAIR8 rRNA:
                  Google
                  TAIR

                  A_thaliana_Jan_2004/
                  -TAIR7 Protein-coding:
                  Google
                  TAIR
                  -TAIR7 miRNA:
                  Google
                  TAIR
                  -TAIR7 rRNA:
                  Google
                  TAIR
                  -TAIR7 tRNA:
                  Google
                  TAIR
                  -TAIR7 other RNA:
                  Google
                  TAIR
                  -TAIR7 snoRNA:
                  Google
                  TAIR
                  -TAIR7 pseudogenes:
                  Google
                  TAIR
                  -TAIR7 snRNAs:
                  Google
                  TAIR

                  A_thaliana_Jun_2009/
                  -TDNA insertion lines:
                  Google
                  -Affymetrix:
                  ATH1 probe sets:
                  Google
                  AG probe sets:
                  Google
                  -TAIR 10 mRNA:
                  Google
                  TAIR
                  -TAIR10 other annotations:
                  -All Genes:
                  Google
                  TAIR
                  -Transposable Elements:
                  Google
                  -TE Genes:
                  Google
                  TAIR
                  -miRNA genes:
                  Google
                  TAIR
                  -ncRNA genes:
                  Google
                  TAIR
                  -pseudogenes:
                  Google
                  TAIR
                  -rRNA genes:
                  Google
                  TAIR
                  -tRNA genes:
                  Google
                  TAIR
                  -snRNA genes:
                  Google
                  TAIR
                  -EST:
                  NCBI EST (single-mapping):
                  Google
                  NCBI EST (multi-mapping):
                  Google
                  -TAIR9:
                  -TAIR9 All:
                  Google
                  TAIR
                  -TAIR9 mRNA:
                  Google
                  TAIR
                  -TAIR9 TE gene:
                  Google
                  TAIR
                  -TAIR9 tRNA:
                  Google
                  TAIR
                  -TAIR9 rRNA:
                  Google
                  TAIR
                  -TAIR9 miRNA:
                  Google
                  TAIR
                  -TAIR9 snoRNA:
                  Google
                  TAIR
                  -TAIR9 snRNA:
                  Google
                  TAIR
                  -TAIR9 ncRNA:
                  Google
                  TAIR

                  B_distachyon_Aug_2010/
                  -Phytozome v7:
                  Google

                  B_taurus_Oct_2011/
                  -RefGene:
                  Google
                  NCBI
                  -mRNA:
                  Google
                  NCBI
                  -EST:
                  Google
                  NCBI

                  C_albicans_SC5314_Nov_2008/
                  -Candidagenome.org:
                  Google

                  C_albicans_WO-1_Jul_2010/ (Genome Sequence exists, but no annotations; NOT an error)

                  C_elegans_May_2008/
                  -RefSeq Genes:
                  Google
                  -WormBase Genes:
                  Google
                  -WormBase PseudoGenes:
                  Google

                  C_elegans_Oct_2010/
                  -RefGene:
                  Google
                  NCBI
                  -mRNA:
                  Google
                  NCBI
                  -EST:
                  Google
                  NCBI

                  C_papaya_Aug_2010/
                  -Phytozome v7:
                  Google

                  C_porcellus_Feb_2008/
                  -RefGene:
                  Google
                  NCBI
                  -mRNA:
                  Google
                  NCBI
                  -EST:
                  Google
                  NCBI

                  C_reinhardtii_Nov_2010/
                  -Phytozome v7:
                  Google

                  D_discoideum_Ax4_May_2009/
                  -All:
                  DictyBase
                  Google
                  -Gene predictions:
                  DictyBase
                  Google
                  -Curated genes (July 2010):
                  DictyBase
                  Google
                  -Geneid re-predictions:
                  DictyBase
                  Google
                  -tRNAs from tRNAscan-SE:
                  DictyBase
                  Google
                  -ncRNAs:
                  DictyBase
                  Google
                  -ncRNAs (Genbank):
                  DictyBase
                  Google

                  D_melanogaster_Apr_2006/
                  -RefGene:
                  Google
                  NCBI
                  -mRNA:
                  Google
                  NCBI
                  -EST:
                  Google
                  NCBI

                  D_rerio_Jul_2010/
                  -RefGene:
                  Google
                  NCBI
                  -mRNA:
                  Google
                  NCBI
                  -EST:
                  Google
                  NCBI

                  E_caballus_Sep_2007/
                  -RefGene:
                  Google
                  NCBI
                  -mRNA:
                  Google (No results)
                  NCBI (strange since Google could not find the page; maybe Google has not yet indexed NCBI page)
                  -EST:
                  Google
                  NCBI

                  E_coli_K12-MG1655_Jan_2012/
                  -Genbank Complete Record:
                  Google

                  F_catus_Dec_2008/
                  -RefGene:
                  Google
                  NCBI
                  -mRNA:
                  Google
                  NCBI
                  -EST:
                  Google
                  NCBI

                  F_catus_Sep_2011/
                  -RefGene:
                  Google
                  NCBI
                  -mRNA:
                  Google
                  NCBI
                  -EST:
                  Google
                  NCBI

                  F_vesca_Sep_2011/
                  -Gene predictions:
                  Google

                  G_gallus_Nov_2011/
                  -RefGene:
                  Google
                  NCBI
                  -mRNA:
                  Google
                  NCBI
                  -EST:
                  Google
                  NCBI

                  G_max_Aug_2010/
                  -Phytozome:
                  Google

                  H_sapiens_Dec_2013/
                  -Cytobands:
                  Google
                  -RefGene:
                  Google
                  NCBI
                  -mRNA:
                  Google
                  NCBI
                  -EST:
                  Google
                  NCBI

                  H_sapiens_Feb_2009/
                  -Cytobands:
                  Google
                  -RefGene:
                  Google
                  NCBI
                  -mRNA:
                  Google
                  NCBI
                  -EST:
                  Google
                  NCBI

                  H_sapiens_Mar_2006/
                  -Cytobands:
                  Google
                  -RefGene:
                  Google
                  NCBI

                  H_sapiens_May_2004/
                  -Cytobands:
                  Google
                  -RefGene:
                  Google
                  NCBI

                  L_africana_Jul_2009/
                  -EnsGene:
                  Google
                  -mRNA:
                  Google
                  NCBI

                  M_domestica_Oct_2006/
                  -RefGene:
                  Google
                  NCBI
                  -mRNA:
                  Google
                  NCBI
                  -EST:
                  Google
                  NCBI

                  M_musculus_Dec_2011/
                  -RefGene:
                  Google
                  NCBI
                  -mRNA:
                  Google
                  NCBI
                  -EST:
                  Google
                  NCBI

                  M_musculus_Jul_2007/
                  -RefGene:
                  Google
                  NCBI
                  -mRNA:
                  Google
                  NCBI
                  -EST:
                  Google
                  NCBI

                  M_truncatula_Mar_2009/
                  -Phytozome v7:
                  Google

                  N_vectensis_Jun_2007/
                  -Gene models:
                  Google (irrelevant search)

                  O_aries_Feb_2010/
                  -RefGene:
                  Google
                  NCBI
                  -mRNA:
                  Google
                  NCBI
                  -EST:
                  Google
                  NCBI

                  O_sativa_japonica_Jun_2009/
                  -Phytozome v7:
                  Google

                  O_sativa_japonica_Oct_2011/
                  -RGAP (MSU7):
                  Google
                  -RAP-DB:
                  Google

                  P_patens_Jan_2008/
                  -CosMoss Gene Models, v1.6:
                  Google

                  P_persica_Apr_2010/
                  -Phytozome v7:
                  Google

                  P_trichocarpa_Aug_2012/
                  -Phytozome:
                  Google

                  P_trichocarpa_Jan_2010/
                  -Phytozome v7:
                  Google

                  P_troglodytes_Oct_2010/
                  -RefGene:
                  Google
                  NCBI
                  -mRNA:
                  Google
                  NCBI
                  -EST:
                  Google
                  NCBI

                  R_communis_May_2008/
                  -Phtyozome v7:
                  Google

                  R_norvegicus_Mar_2012/
                  -RefGene:
                  Google
                  NCBI
                  -mRNA:
                  Google
                  NCBI
                  -EST:
                  Google
                  NCBI

                  S_bicolor_Jan_2009/
                  -Phytozome v7:
                  Google

                  S_cerevisiae_Apr_2011/
                  -Genes:
                  Google
                  SGD

                  S_lycopersicum_Feb_2014/
                  -ITAG2.4:
                  Google

                  S_lycopersicum_May_2012/
                  -ITAG2.3:
                  Google

                  S_pombe_May_2012/
                  -Reference genes:
                  Google

                  T_castaneum_Mar_2008/
                  -Reference genes:
                  Google
                  -Scaffold Regions:
                  Google

                  T_kodakaraensis_KOD1_May_2004/
                  -Gene:
                  Google

                  T_parvula_May_2012/
                  -FGenesh++:
                  Google

                  T_rubripes_Oct_2011/
                  -RefGene:
                  Google
                  NCBI
                  -mRNA:
                  Google
                  NCBI
                  -EST:
                  Google
                  NCBI

                  V_carteri_Jul_2010/
                  -Phytozome v7:
                  Google (irrelevant search)

                  V_vinifera_Mar_2010/
                  -Phytozome v7:
                  Google

                  X_tropicalis_Nov_2009/
                  -RefGene:
                  Google
                  NCBI
                  -mRNA:
                  Google
                  NCBI
                  -EST:
                  Google
                  NCBI

                  Z_mays_B73_Mar_2010/
                  -Maize Transcripts 5b release:
                  Google
                  MaizeSequence.org

                  Show
                  mason Mason Meyer (Inactive) added a comment - - edited *Recommendations from this testing for more accurate search results: 1) We should add the description and species to the Gene ID in the Google search. 2) We should convert underscores to spaces for Google search. A_gambiae_Feb_2003/ -EnsGene: Google -mRNA: Google NCBI -EST: Google NCBI A_lyrata_Apr_2011/ -Phytozome v7: Google (irrelevant search) A_melanoleuca_Dec_2009/ -EnsGene: Google -mRNA: Google NCBI -EST: Google NCBI A_mellifera_Jan_2005/ -RefGene: Google *Ex: AmeLGUn_WGA742_2.501998.501998.m (from Richard Linchancgo's testing) *The underscores should actually be converted to spaces for Google NCBI (inconsistent behavior; several broken links) -mRNA: Google NCBI -EST: Google NCBI A_thaliana_Apr_2008/ -TAIR8 mRNA: Google TAIR -TAIR8 tRNA: Google TAIR -TAIR8 miRNA: Google TAIR -TAIR8 ncRNA: Google TAIR -TAIR8 snRNA: Google TAIR -TAIR8 snoRNA: Google TAIR -TAIR8 rRNA: Google TAIR A_thaliana_Jan_2004/ -TAIR7 Protein-coding: Google TAIR -TAIR7 miRNA: Google TAIR -TAIR7 rRNA: Google TAIR -TAIR7 tRNA: Google TAIR -TAIR7 other RNA: Google TAIR -TAIR7 snoRNA: Google TAIR -TAIR7 pseudogenes: Google TAIR -TAIR7 snRNAs: Google TAIR A_thaliana_Jun_2009/ -TDNA insertion lines: Google -Affymetrix: ATH1 probe sets: Google AG probe sets: Google -TAIR 10 mRNA: Google TAIR -TAIR10 other annotations: -All Genes: Google TAIR -Transposable Elements: Google -TE Genes: Google TAIR -miRNA genes: Google TAIR -ncRNA genes: Google TAIR -pseudogenes: Google TAIR -rRNA genes: Google TAIR -tRNA genes: Google TAIR -snRNA genes: Google TAIR -EST: NCBI EST (single-mapping): Google NCBI EST (multi-mapping): Google -TAIR9: -TAIR9 All: Google TAIR -TAIR9 mRNA: Google TAIR -TAIR9 TE gene: Google TAIR -TAIR9 tRNA: Google TAIR -TAIR9 rRNA: Google TAIR -TAIR9 miRNA: Google TAIR -TAIR9 snoRNA: Google TAIR -TAIR9 snRNA: Google TAIR -TAIR9 ncRNA: Google TAIR B_distachyon_Aug_2010/ -Phytozome v7: Google B_taurus_Oct_2011/ -RefGene: Google NCBI -mRNA: Google NCBI -EST: Google NCBI C_albicans_SC5314_Nov_2008/ -Candidagenome.org: Google C_albicans_WO-1_Jul_2010/ (Genome Sequence exists, but no annotations; NOT an error) C_elegans_May_2008/ -RefSeq Genes: Google -WormBase Genes: Google -WormBase PseudoGenes: Google C_elegans_Oct_2010/ -RefGene: Google NCBI -mRNA: Google NCBI -EST: Google NCBI C_papaya_Aug_2010/ -Phytozome v7: Google C_porcellus_Feb_2008/ -RefGene: Google NCBI -mRNA: Google NCBI -EST: Google NCBI C_reinhardtii_Nov_2010/ -Phytozome v7: Google D_discoideum_Ax4_May_2009/ -All: DictyBase Google -Gene predictions: DictyBase Google -Curated genes (July 2010): DictyBase Google -Geneid re-predictions: DictyBase Google -tRNAs from tRNAscan-SE: DictyBase Google -ncRNAs: DictyBase Google -ncRNAs (Genbank): DictyBase Google D_melanogaster_Apr_2006/ -RefGene: Google NCBI -mRNA: Google NCBI -EST: Google NCBI D_rerio_Jul_2010/ -RefGene: Google NCBI -mRNA: Google NCBI -EST: Google NCBI E_caballus_Sep_2007/ -RefGene: Google NCBI -mRNA: Google (No results) NCBI (strange since Google could not find the page; maybe Google has not yet indexed NCBI page) -EST: Google NCBI E_coli_K12-MG1655_Jan_2012/ -Genbank Complete Record: Google F_catus_Dec_2008/ -RefGene: Google NCBI -mRNA: Google NCBI -EST: Google NCBI F_catus_Sep_2011/ -RefGene: Google NCBI -mRNA: Google NCBI -EST: Google NCBI F_vesca_Sep_2011/ -Gene predictions: Google G_gallus_Nov_2011/ -RefGene: Google NCBI -mRNA: Google NCBI -EST: Google NCBI G_max_Aug_2010/ -Phytozome: Google H_sapiens_Dec_2013/ -Cytobands: Google -RefGene: Google NCBI -mRNA: Google NCBI -EST: Google NCBI H_sapiens_Feb_2009/ -Cytobands: Google -RefGene: Google NCBI -mRNA: Google NCBI -EST: Google NCBI H_sapiens_Mar_2006/ -Cytobands: Google -RefGene: Google NCBI H_sapiens_May_2004/ -Cytobands: Google -RefGene: Google NCBI L_africana_Jul_2009/ -EnsGene: Google -mRNA: Google NCBI M_domestica_Oct_2006/ -RefGene: Google NCBI -mRNA: Google NCBI -EST: Google NCBI M_musculus_Dec_2011/ -RefGene: Google NCBI -mRNA: Google NCBI -EST: Google NCBI M_musculus_Jul_2007/ -RefGene: Google NCBI -mRNA: Google NCBI -EST: Google NCBI M_truncatula_Mar_2009/ -Phytozome v7: Google N_vectensis_Jun_2007/ -Gene models: Google (irrelevant search) O_aries_Feb_2010/ -RefGene: Google NCBI -mRNA: Google NCBI -EST: Google NCBI O_sativa_japonica_Jun_2009/ -Phytozome v7: Google O_sativa_japonica_Oct_2011/ -RGAP (MSU7): Google -RAP-DB: Google P_patens_Jan_2008/ -CosMoss Gene Models, v1.6: Google P_persica_Apr_2010/ -Phytozome v7: Google P_trichocarpa_Aug_2012/ -Phytozome: Google P_trichocarpa_Jan_2010/ -Phytozome v7: Google P_troglodytes_Oct_2010/ -RefGene: Google NCBI -mRNA: Google NCBI -EST: Google NCBI R_communis_May_2008/ -Phtyozome v7: Google R_norvegicus_Mar_2012/ -RefGene: Google NCBI -mRNA: Google NCBI -EST: Google NCBI S_bicolor_Jan_2009/ -Phytozome v7: Google S_cerevisiae_Apr_2011/ -Genes: Google SGD S_lycopersicum_Feb_2014/ -ITAG2.4: Google S_lycopersicum_May_2012/ -ITAG2.3: Google S_pombe_May_2012/ -Reference genes: Google T_castaneum_Mar_2008/ -Reference genes: Google -Scaffold Regions: Google T_kodakaraensis_KOD1_May_2004/ -Gene: Google T_parvula_May_2012/ -FGenesh++: Google T_rubripes_Oct_2011/ -RefGene: Google NCBI -mRNA: Google NCBI -EST: Google NCBI V_carteri_Jul_2010/ -Phytozome v7: Google (irrelevant search) V_vinifera_Mar_2010/ -Phytozome v7: Google X_tropicalis_Nov_2009/ -RefGene: Google NCBI -mRNA: Google NCBI -EST: Google NCBI Z_mays_B73_Mar_2010/ -Maize Transcripts 5b release: Google MaizeSequence.org

                    People

                    • Assignee:
                      mason Mason Meyer (Inactive)
                      Reporter:
                      hiralv Hiral Vora (Inactive)
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                      • Created:
                        Updated: