Details
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Type: Task
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Status: Closed (View Workflow)
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Priority: Major
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Resolution: Done
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Affects Version/s: None
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Fix Version/s: None
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Labels:
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Story Points:1
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Epic Link:
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Sprint:Spring 4 2023 Feb 21, Spring 5 2023 Mar 6
Description
[~aloraine] agreed to review an article that describes a new iteration of "CHESS" annotations for human genome. Review is due 19 Feb 2023. Article info:
- Web site with annotations: http://ccb.jhu.edu/chess/
- Article draft on BioRxiv: https://www.biorxiv.org/content/10.1101/2022.12.21.521274v1
Preliminary scan of the article shows that these new annotations could be very useful for understanding human transcriptome, so this task also includes deploying the annotations into IGB Quickload site.
Proposed strategy for reviewing this work:
- Try to deploy the annotations onto an IGB Quickload site
- If that goes well, use IGB to make interesting and/or artistic screen shots of genomic scenes showing the CHESS data
- Submit a review that describes observations made
Possible benefits of proposed strategy:
- Helps bioinformatics scientists by pointing out a useful dataset or helping to improve a work in progress
- Try out a possible new use case for IGB (dataset review tool?)
- Provide access to possibly very useful gene models that can benefit our field, and others
Attachments
Issue Links
- relates to
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IGBF-3288 Add CHM13 and CHESS for CHM13 to IGB
- To-Do
Activity
Ann Loraine
created issue -
Ann Loraine
made changes -
Field | Original Value | New Value |
---|---|---|
Epic Link | IGBF-1765 [ 17855 ] |
Ann Loraine
made changes -
Sprint | Spring 3 2023 Feb 1 [ 163 ] | |
Labels | Advanced |
Ann Loraine
made changes -
Description |
[~aloraine] agreed to review an article that describes a new iteration of "CHESS" annotations. Review is due 19 Feb 2023. Article info:
* Web site with annotations: http://ccb.jhu.edu/chess/ * Article draft on BioRxiv: https://www.biorxiv.org/content/10.1101/2022.12.21.521274v1 |
[~aloraine] agreed to review an article that describes a new iteration of "CHESS" annotations for human genome. Review is due 19 Feb 2023. Article info:
* Web site with annotations: http://ccb.jhu.edu/chess/ * Article draft on BioRxiv: https://www.biorxiv.org/content/10.1101/2022.12.21.521274v1 Preliminary scan of the article shows that these new annotations could be very useful for understanding human transcriptome, so this task also includes deploying the annotations into IGB Quickload site. |
Ann Loraine
made changes -
Description |
[~aloraine] agreed to review an article that describes a new iteration of "CHESS" annotations for human genome. Review is due 19 Feb 2023. Article info:
* Web site with annotations: http://ccb.jhu.edu/chess/ * Article draft on BioRxiv: https://www.biorxiv.org/content/10.1101/2022.12.21.521274v1 Preliminary scan of the article shows that these new annotations could be very useful for understanding human transcriptome, so this task also includes deploying the annotations into IGB Quickload site. |
[~aloraine] agreed to review an article that describes a new iteration of "CHESS" annotations for human genome. Review is due 19 Feb 2023. Article info:
* Web site with annotations: http://ccb.jhu.edu/chess/ * Article draft on BioRxiv: https://www.biorxiv.org/content/10.1101/2022.12.21.521274v1 Preliminary scan of the article shows that these new annotations could be very useful for understanding human transcriptome, so this task also includes deploying the annotations into IGB Quickload site. Proposed strategy for reviewing this work: * Try to deploy the annotations onto an IGB Quickload site * If that goes well, use IGB to make interesting and/or artistic screen shots of genomic scenes showing the CHESS data * Submit a review that describes observations made Possible benefits of proposed strategy: * Helps bioinformatics scientists by pointing out a useful dataset *or* helping to improve a work in progress * Try out a possible new use case for IGB (dataset review tool?) * Provide access to possibly very useful gene models that can benefit our field, and others |
Ann Loraine
made changes -
Sprint | Spring 3 2023 Feb 1 [ 163 ] | Spring 4 2023 Feb 13 [ 164 ] |
Ann Loraine
made changes -
Summary | Write review for CHESS article | Add CHESS to IGB and write review |
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] |
Ann Loraine
made changes -
Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] |
Ann Loraine
made changes -
Status | In Progress [ 3 ] | To-Do [ 10305 ] |
Ann Loraine
made changes -
Status | To-Do [ 10305 ] | In Progress [ 3 ] |
Ann Loraine
made changes -
Comment |
[ Sometimes there are missing values in the extra feature field:{code}
chr1 Curated Genomic transcript 63016 63885 . + . ID=CHS.144070.2;geneID=CHS.144070;gene_name=OR4G11P;gene_type=pseudogene;db_xref {code} Here, "db_xref" is listed but has no value. Why not? ] |
Ann Loraine
made changes -
Comment |
[ Made git repository to manage and host new QL site:
* https://bitbucket.org/lorainelab/chess-quickload-for-igb/src/main/ ] |
Ann Loraine
made changes -
Attachment | chess-chr1.png [ 17712 ] |
Ann Loraine
made changes -
Attachment | titin.png [ 17713 ] |
Ann Loraine
made changes -
Ann Loraine
made changes -
Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] |
Ann Loraine
made changes -
Sprint | Spring 4 2023 Feb 21 [ 164 ] | Spring 4 2023 Feb 21, Spring 5 2023 Mar 6 [ 164, 165 ] |
Ann Loraine
made changes -
Rank | Ranked higher |
Ann Loraine
made changes -
Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
Ann Loraine
made changes -
Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
Ann Loraine
made changes -
Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
Ann Loraine
made changes -
Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
Ann Loraine
made changes -
Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
Ann Loraine
made changes -
Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
Ann Loraine
made changes -
Resolution | Done [ 10000 ] | |
Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
Ann Loraine
made changes -
Assignee | Ann Loraine [ aloraine ] |
Ann Loraine
made changes -
Summary | Add CHESS to IGB and write review | Add CHESS to IGB Quickload for hg38 |
Contacted authors to find out location of reference assembly used to generate the annotations. Answer is: