Details
-
Type:
Task
-
Status: Closed (View Workflow)
-
Priority:
Major
-
Resolution: Done
-
Affects Version/s: None
-
Fix Version/s: None
-
Labels:
-
Story Points:1
-
Epic Link:
-
Sprint:Spring 4 2023 Feb 21, Spring 5 2023 Mar 6
Description
Ann Loraine 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
-
-
- To-Do
-
Activity
| Field | Original Value | New Value |
|---|---|---|
| Epic Link | IGBF-1765 [ 17855 ] |
| Sprint | Spring 3 2023 Feb 1 [ 163 ] | |
| Labels | Advanced |
| 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. |
| 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 |
| Sprint | Spring 3 2023 Feb 1 [ 163 ] | Spring 4 2023 Feb 13 [ 164 ] |
| Summary | Write review for CHESS article | Add CHESS to IGB and write review |
| Assignee | Ann Loraine [ aloraine ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Status | In Progress [ 3 ] | To-Do [ 10305 ] |
| Status | To-Do [ 10305 ] | In Progress [ 3 ] |
| 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? ] |
| Comment |
[ Made git repository to manage and host new QL site:
* https://bitbucket.org/lorainelab/chess-quickload-for-igb/src/main/ ] |
| Attachment | chess-chr1.png [ 17712 ] |
| Attachment | titin.png [ 17713 ] |
| Status | In Progress [ 3 ] | Needs 1st Level Review [ 10005 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Sprint | Spring 4 2023 Feb 21 [ 164 ] | Spring 4 2023 Feb 21, Spring 5 2023 Mar 6 [ 164, 165 ] |
| Rank | Ranked higher |
| Status | Needs 1st Level Review [ 10005 ] | First Level Review in Progress [ 10301 ] |
| Status | First Level Review in Progress [ 10301 ] | Ready for Pull Request [ 10304 ] |
| Status | Ready for Pull Request [ 10304 ] | Pull Request Submitted [ 10101 ] |
| Status | Pull Request Submitted [ 10101 ] | Reviewing Pull Request [ 10303 ] |
| Status | Reviewing Pull Request [ 10303 ] | Merged Needs Testing [ 10002 ] |
| Status | Merged Needs Testing [ 10002 ] | Post-merge Testing In Progress [ 10003 ] |
| Resolution | Done [ 10000 ] | |
| Status | Post-merge Testing In Progress [ 10003 ] | Closed [ 6 ] |
| Assignee | Ann Loraine [ aloraine ] |
| Summary | Add CHESS to IGB and write review | Add CHESS to IGB Quickload for hg38 |