https://wiki.wormbase.org/api.php?action=feedcontributions&user=Pnuin&feedformat=atomWormBaseWiki - User contributions [en]2024-03-29T12:34:13ZUser contributionsMediaWiki 1.33.0https://wiki.wormbase.org/index.php?title=WBConfCall_2023.11.16-Agenda_and_Minutes&diff=38210WBConfCall 2023.11.16-Agenda and Minutes2023-11-16T17:43:50Z<p>Pnuin: /* New objects form */</p>
<hr />
<div>==Agenda/Minutes==<br />
<br />
<br />
AGR Paper - soft deadline for edits is this Friday, but some modifications can be made next week.<br />
<br />
https://docs.google.com/document/d/1SC_zEBCes7l2ifqIEYljaMs7Orc3kklw<br />
<br />
WB paper - deadline would be to early December. Focus is on the transition of data, resources and infrastructure from WormBase to the Alliance. Still more a planning document than a finished paper. Everyone should check the document and add things to be discussed, paragraphs or aspects to be added.<br />
<br />
<br />
https://docs.google.com/document/d/1ecpa8MVYGYTvFvXRDMb0EZitaO3W7L2D2hdDCbH2Cv0/edit<br />
<br />
=New objects form=<br />
* We will need a replacement for the New object CGI<br />
<br />
Javascript libraries provide by Google will be sunsetted, so there's a work on fixing for the Name server UI. There will be locks required in order for data created in the standard UI tom be loaded into Postgres. There will be a requirement to write code to send data from the curation side to Postgres.<br />
<br />
<br />
Check following link for the soon to be deprecated libraries<br />
<br />
https://developers.google.com/identity/sign-in/web/deprecation-and-sunset<br />
<br />
=Data freeze / Upload=<br />
* Up to Caltech, but be aware that SKD will be on vacation from Dec-4 till Jan-4. After that ~ 2 weeks required for Dec updates and prebuild so Main build most likely won't start by mid January.<br />
<br />
<br />
January is fine for data upload to CalTech.<br />
<br />
<br />
=Apollo @ WormBase=<br />
* SKD -> Scott and WebTeam: Is it possible to run Apollo on top of our JBrowse? Can be internally only.<br />
<br />
Scott will check the possibility of running a container with Appolo v2 on top of JBrowse.</div>Pnuinhttps://wiki.wormbase.org/index.php?title=WBConfCall_2023.11.16-Agenda_and_Minutes&diff=38209WBConfCall 2023.11.16-Agenda and Minutes2023-11-16T17:43:12Z<p>Pnuin: </p>
<hr />
<div>==Agenda/Minutes==<br />
<br />
<br />
AGR Paper - soft deadline for edits is this Friday, but some modifications can be made next week.<br />
<br />
https://docs.google.com/document/d/1SC_zEBCes7l2ifqIEYljaMs7Orc3kklw<br />
<br />
WB paper - deadline would be to early December. Focus is on the transition of data, resources and infrastructure from WormBase to the Alliance. Still more a planning document than a finished paper. Everyone should check the document and add things to be discussed, paragraphs or aspects to be added.<br />
<br />
<br />
https://docs.google.com/document/d/1ecpa8MVYGYTvFvXRDMb0EZitaO3W7L2D2hdDCbH2Cv0/edit<br />
<br />
=New objects form=<br />
* We will need a replacement for the New object CGI<br />
<br />
Javascript libraries provide by Google will be sunsetted, so there's a work on fixing for the Name server UI. There will be locks required in order for data created in the standard UI tom be loaded into Postgres. There will be a requirement to write code to send data from the curation side to Postgres.<br />
<br />
<br />
https://developers.google.com/identity/sign-in/web/deprecation-and-sunset<br />
<br />
<br />
=Data freeze / Upload=<br />
* Up to Caltech, but be aware that SKD will be on vacation from Dec-4 till Jan-4. After that ~ 2 weeks required for Dec updates and prebuild so Main build most likely won't start by mid January.<br />
<br />
<br />
January is fine for data upload to CalTech.<br />
<br />
<br />
=Apollo @ WormBase=<br />
* SKD -> Scott and WebTeam: Is it possible to run Apollo on top of our JBrowse? Can be internally only.<br />
<br />
Scott will check the possibility of running a container with Appolo v2 on top of JBrowse.</div>Pnuinhttps://wiki.wormbase.org/index.php?title=WBConfCall_2023.11.16-Agenda_and_Minutes&diff=38208WBConfCall 2023.11.16-Agenda and Minutes2023-11-16T16:50:04Z<p>Pnuin: /* Agenda/Minutes */</p>
<hr />
<div>==Agenda/Minutes==<br />
<br />
<br />
AGR Paper<br />
<br />
<br />
WB paper<br />
<br />
https://docs.google.com/document/d/1ecpa8MVYGYTvFvXRDMb0EZitaO3W7L2D2hdDCbH2Cv0/edit<br />
<br />
=New objects form=<br />
* We will need a replacement for the New object CGI<br />
<br />
https://developers.google.com/identity/sign-in/web/deprecation-and-sunset<br />
<br />
<br />
=Data freeze / Upload=<br />
* Up to Caltech, but be aware that SKD will be on vacation from Dec-4 till Jan-4. After that ~ 2 weeks required for Dec updates and prebuild so Main build most likely won't start by mid January.<br />
<br />
=Apollo @ WormBase=<br />
* SKD -> Scott and WebTeam: Is it possible to run Apollo on top of our JBrowse? Can be internally only.</div>Pnuinhttps://wiki.wormbase.org/index.php?title=WBConfCall_2023.11.16-Agenda_and_Minutes&diff=38207WBConfCall 2023.11.16-Agenda and Minutes2023-11-16T16:46:34Z<p>Pnuin: /* Agenda/Minutes */</p>
<hr />
<div>==Agenda/Minutes==<br />
<br />
<br />
AGR Paper<br />
<br />
<br />
WB paper<br />
<br />
=New objects form=<br />
* We will need a replacement for the New object CGI<br />
<br />
https://developers.google.com/identity/sign-in/web/deprecation-and-sunset<br />
<br />
<br />
=Data freeze / Upload=<br />
* Up to Caltech, but be aware that SKD will be on vacation from Dec-4 till Jan-4. After that ~ 2 weeks required for Dec updates and prebuild so Main build most likely won't start by mid January.<br />
<br />
=Apollo @ WormBase=<br />
* SKD -> Scott and WebTeam: Is it possible to run Apollo on top of our JBrowse? Can be internally only.</div>Pnuinhttps://wiki.wormbase.org/index.php?title=WBConfCall_2023.11.16-Agenda_and_Minutes&diff=38206WBConfCall 2023.11.16-Agenda and Minutes2023-11-16T16:46:15Z<p>Pnuin: </p>
<hr />
<div>==Agenda/Minutes==<br />
<br />
<br />
AGR Papep<br />
WB paper<br />
<br />
=New objects form=<br />
* We will need a replacement for the New object CGI<br />
<br />
https://developers.google.com/identity/sign-in/web/deprecation-and-sunset<br />
<br />
<br />
=Data freeze / Upload=<br />
* Up to Caltech, but be aware that SKD will be on vacation from Dec-4 till Jan-4. After that ~ 2 weeks required for Dec updates and prebuild so Main build most likely won't start by mid January.<br />
<br />
=Apollo @ WormBase=<br />
* SKD -> Scott and WebTeam: Is it possible to run Apollo on top of our JBrowse? Can be internally only.</div>Pnuinhttps://wiki.wormbase.org/index.php?title=WBConfCall_2023.11.16-Agenda_and_Minutes&diff=38205WBConfCall 2023.11.16-Agenda and Minutes2023-11-16T16:36:15Z<p>Pnuin: /* Agenda/Minutes */</p>
<hr />
<div>==Agenda/Minutes==<br />
<br />
<br />
AGR Paper<br />
<br />
=New objects form=<br />
* We will need a replacement for the New object CGI<br />
<br />
=Data freeze / Upload=<br />
* Up to Caltech, but be aware that SKD will be on vacation from Dec-4 till Jan-4. After that ~ 2 weeks required for Dec updates and prebuild so Main build most likely won't start by mid January.<br />
<br />
=Apollo @ WormBase=<br />
* SKD -> Scott and WebTeam: Is it possible to run Apollo on top of our JBrowse? Can be internally only.</div>Pnuinhttps://wiki.wormbase.org/index.php?title=WBConfCall_2023.03.16-Agenda_and_Minutes&diff=37806WBConfCall 2023.03.16-Agenda and Minutes2023-03-16T16:18:16Z<p>Pnuin: New items</p>
<hr />
<div>= Agenda =<br />
<br />
== Help Desk ==<br />
<br />
1. Cristian Riccio (Miska Lab): whole genome assemblies of 18 wild isolates. Should we host?<br />
<br />
- Sarah contacted Cristian, who works in Cambridge and she will provide more information. One option is to provide JBrowse tracks.<br />
<br />
== IWM 2023 ==<br />
* Who is going?<br />
<br />
- Roster will be created to line up speakers, presentations, etc. <br />
- Pre registration is May 2nd'<br />
- travel funds were discussed<br />
<br />
== Alliance/Caltech Literature ==<br />
* Caltech created a parallel PubMed search pipeline and paper editor UI for WormBase Parasite<br />
* Is this still being used?<br />
<br />
- Discussion was what should be done with the Lit. branch for ParaSite. Dionysis will take a look and discuss with Kimberly.<br />
<br />
== Grants for AI/ML Readiness of Data ==<br />
* [https://grants.nih.gov/grants/guide/notice-files/not-od-23-082.html NOT-OD-23-082- Administrative Supplements to Support Collaborations to Improve the AI/ML-Readiness of NIH-Supported Data]<br />
* Proposal(s) from WB?<br />
<br />
- NIH/NLM provide supplements for making data FAIR or ready for AI/ML ingestion, and proposals can be quite open and broad as there's no consensus from the funding agencies on what is the best approach. Gene ontology seems like a good initial candidate.<br />
<br />
- Other MODs can also work on getting supplemental funding<br />
<br />
== Bob Waterston single cell data ==<br />
* Data on staging<br />
* Bob said it looks great - also shared with his lab and John Murray <br />
* He asks if i)use log scale ii)display above CenGen and iii) if we want the L2 dataset from the 2017 paper in a similar format<br />
<br />
- on i) there are dose discussions on how to setup a log display and some possibilities will be discussed and checked on the JS graphing library<br />
- on ii) CenGen should be on top as it's the latests data available<br />
- on iii) we might consider requesting the data and working on a similar display<br />
<br />
More discussions:<br />
- labelling/values consistency with CenGen graphs<br />
- embryonic cell on top of lineage<br />
- display/link static images<br />
<br />
== New items ==<br />
<br />
* Paul brought up a discussion on adding new genomes/species to WormBase, including setting up Tier 1, 2 species. This discussion should be done in conjunction to WB's advisory board and meeting(s) should be scheduled in order for the conversations and plan to be defined.</div>Pnuinhttps://wiki.wormbase.org/index.php?title=WBConfCall_2023.03.16-Agenda_and_Minutes&diff=37805WBConfCall 2023.03.16-Agenda and Minutes2023-03-16T16:15:32Z<p>Pnuin: /* Bob Waterston single cell data */</p>
<hr />
<div>= Agenda =<br />
<br />
== Help Desk ==<br />
<br />
1. Cristian Riccio (Miska Lab): whole genome assemblies of 18 wild isolates. Should we host?<br />
<br />
- Sarah contacted Cristian, who works in Cambridge and she will provide more information. One option is to provide JBrowse tracks.<br />
<br />
== IWM 2023 ==<br />
* Who is going?<br />
<br />
- Roster will be created to line up speakers, presentations, etc. <br />
- Pre registration is May 2nd'<br />
- travel funds were discussed<br />
<br />
== Alliance/Caltech Literature ==<br />
* Caltech created a parallel PubMed search pipeline and paper editor UI for WormBase Parasite<br />
* Is this still being used?<br />
<br />
- Discussion was what should be done with the Lit. branch for ParaSite. Dionysis will take a look and discuss with Kimberly.<br />
<br />
== Grants for AI/ML Readiness of Data ==<br />
* [https://grants.nih.gov/grants/guide/notice-files/not-od-23-082.html NOT-OD-23-082- Administrative Supplements to Support Collaborations to Improve the AI/ML-Readiness of NIH-Supported Data]<br />
* Proposal(s) from WB?<br />
<br />
- NIH/NLM provide supplements for making data FAIR or ready for AI/ML ingestion, and proposals can be quite open and broad as there's no consensus from the funding agencies on what is the best approach. Gene ontology seems like a good initial candidate.<br />
<br />
- Other MODs can also work on getting supplemental funding<br />
<br />
== Bob Waterston single cell data ==<br />
* Data on staging<br />
* Bob said it looks great - also shared with his lab and John Murray <br />
* He asks if i)use log scale ii)display above CenGen and iii) if we want the L2 dataset from the 2017 paper in a similar format<br />
<br />
- on i) there are dose discussions on how to setup a log display and some possibilities will be discussed and checked on the JS graphing library<br />
- on ii) CenGen should be on top as it's the latests data available<br />
- on iii) we might consider requesting the data and working on a similar display<br />
<br />
More discussions:<br />
- labelling/values consistency with CenGen graphs<br />
- embryonic cell on top of lineage<br />
- display/link static images</div>Pnuinhttps://wiki.wormbase.org/index.php?title=WBConfCall_2023.03.16-Agenda_and_Minutes&diff=37804WBConfCall 2023.03.16-Agenda and Minutes2023-03-16T16:11:58Z<p>Pnuin: /* Grants for AI/ML Readiness of Data */</p>
<hr />
<div>= Agenda =<br />
<br />
== Help Desk ==<br />
<br />
1. Cristian Riccio (Miska Lab): whole genome assemblies of 18 wild isolates. Should we host?<br />
<br />
- Sarah contacted Cristian, who works in Cambridge and she will provide more information. One option is to provide JBrowse tracks.<br />
<br />
== IWM 2023 ==<br />
* Who is going?<br />
<br />
- Roster will be created to line up speakers, presentations, etc. <br />
- Pre registration is May 2nd'<br />
- travel funds were discussed<br />
<br />
== Alliance/Caltech Literature ==<br />
* Caltech created a parallel PubMed search pipeline and paper editor UI for WormBase Parasite<br />
* Is this still being used?<br />
<br />
- Discussion was what should be done with the Lit. branch for ParaSite. Dionysis will take a look and discuss with Kimberly.<br />
<br />
== Grants for AI/ML Readiness of Data ==<br />
* [https://grants.nih.gov/grants/guide/notice-files/not-od-23-082.html NOT-OD-23-082- Administrative Supplements to Support Collaborations to Improve the AI/ML-Readiness of NIH-Supported Data]<br />
* Proposal(s) from WB?<br />
<br />
- NIH/NLM provide supplements for making data FAIR or ready for AI/ML ingestion, and proposals can be quite open and broad as there's no consensus from the funding agencies on what is the best approach. Gene ontology seems like a good initial candidate.<br />
<br />
- Other MODs can also work on getting supplemental funding<br />
<br />
== Bob Waterston single cell data ==<br />
* Data on staging<br />
* Bob said it looks great - also shared with his lab and John Murray <br />
* He asks if i)use log scale ii)display above CenGen and iii) if we want the L2 dataset from the 2017 paper in a similar format</div>Pnuinhttps://wiki.wormbase.org/index.php?title=WBConfCall_2023.03.16-Agenda_and_Minutes&diff=37803WBConfCall 2023.03.16-Agenda and Minutes2023-03-16T16:09:27Z<p>Pnuin: /* Alliance/Caltech Literature */</p>
<hr />
<div>= Agenda =<br />
<br />
== Help Desk ==<br />
<br />
1. Cristian Riccio (Miska Lab): whole genome assemblies of 18 wild isolates. Should we host?<br />
<br />
- Sarah contacted Cristian, who works in Cambridge and she will provide more information. One option is to provide JBrowse tracks.<br />
<br />
== IWM 2023 ==<br />
* Who is going?<br />
<br />
- Roster will be created to line up speakers, presentations, etc. <br />
- Pre registration is May 2nd'<br />
- travel funds were discussed<br />
<br />
== Alliance/Caltech Literature ==<br />
* Caltech created a parallel PubMed search pipeline and paper editor UI for WormBase Parasite<br />
* Is this still being used?<br />
<br />
- Discussion was what should be done with the Lit. branch for ParaSite. Dionysis will take a look and discuss with Kimberly.<br />
<br />
== Grants for AI/ML Readiness of Data ==<br />
* [https://grants.nih.gov/grants/guide/notice-files/not-od-23-082.html NOT-OD-23-082- Administrative Supplements to Support Collaborations to Improve the AI/ML-Readiness of NIH-Supported Data]<br />
* Proposal(s) from WB?<br />
<br />
== Bob Waterston single cell data ==<br />
* Data on staging<br />
* Bob said it looks great - also shared with his lab and John Murray <br />
* He asks if i)use log scale ii)display above CenGen and iii) if we want the L2 dataset from the 2017 paper in a similar format</div>Pnuinhttps://wiki.wormbase.org/index.php?title=WBConfCall_2023.03.16-Agenda_and_Minutes&diff=37802WBConfCall 2023.03.16-Agenda and Minutes2023-03-16T16:08:04Z<p>Pnuin: /* Help Desk */</p>
<hr />
<div>= Agenda =<br />
<br />
== Help Desk ==<br />
<br />
1. Cristian Riccio (Miska Lab): whole genome assemblies of 18 wild isolates. Should we host?<br />
<br />
- Sarah contacted Cristian, who works in Cambridge and she will provide more information. One option is to provide JBrowse tracks.<br />
<br />
== IWM 2023 ==<br />
* Who is going?<br />
<br />
- Roster will be created to line up speakers, presentations, etc. <br />
- Pre registration is May 2nd'<br />
- travel funds were discussed<br />
<br />
== Alliance/Caltech Literature ==<br />
* Caltech created a parallel PubMed search pipeline and paper editor UI for WormBase Parasite<br />
* Is this still being used?<br />
<br />
== Grants for AI/ML Readiness of Data ==<br />
* [https://grants.nih.gov/grants/guide/notice-files/not-od-23-082.html NOT-OD-23-082- Administrative Supplements to Support Collaborations to Improve the AI/ML-Readiness of NIH-Supported Data]<br />
* Proposal(s) from WB?<br />
<br />
== Bob Waterston single cell data ==<br />
* Data on staging<br />
* Bob said it looks great - also shared with his lab and John Murray <br />
* He asks if i)use log scale ii)display above CenGen and iii) if we want the L2 dataset from the 2017 paper in a similar format</div>Pnuinhttps://wiki.wormbase.org/index.php?title=WBConfCall_2023.03.16-Agenda_and_Minutes&diff=37801WBConfCall 2023.03.16-Agenda and Minutes2023-03-16T16:07:44Z<p>Pnuin: /* IWM 2023 */</p>
<hr />
<div>= Agenda =<br />
<br />
== Help Desk ==<br />
<br />
1. Cristian Riccio (Miska Lab): whole genome assemblies of 18 wild isolates. Should we host?<br />
<br />
- Sarah contacted Cristian, who works in Cambridge and she will provide more information. One option is to provide JBrowse tracks.<br />
<br />
== IWM 2023 ==<br />
* Who is going?<br />
<br />
- Roster will be created to line up speakers, presentations, etc. <br />
- Pre registration is May 2nd'<br />
- travel funds were discussed<br />
<br />
== Alliance/Caltech Literature ==<br />
* Caltech created a parallel PubMed search pipeline and paper editor UI for WormBase Parasite<br />
* Is this still being used?<br />
<br />
== Grants for AI/ML Readiness of Data ==<br />
* [https://grants.nih.gov/grants/guide/notice-files/not-od-23-082.html NOT-OD-23-082- Administrative Supplements to Support Collaborations to Improve the AI/ML-Readiness of NIH-Supported Data]<br />
* Proposal(s) from WB?<br />
<br />
== Bob Waterston single cell data ==<br />
* Data on staging<br />
* Bob said it looks great - also shared with his lab and John Murray <br />
* He asks if i)use log scale ii)display above CenGen and iii) if we want the L2 dataset from the 2017 paper in a similar format</div>Pnuinhttps://wiki.wormbase.org/index.php?title=WBConfCall_2023.03.16-Agenda_and_Minutes&diff=37800WBConfCall 2023.03.16-Agenda and Minutes2023-03-16T16:06:31Z<p>Pnuin: /* Help Desk */</p>
<hr />
<div>= Agenda =<br />
<br />
== Help Desk ==<br />
<br />
1. Cristian Riccio (Miska Lab): whole genome assemblies of 18 wild isolates. Should we host?<br />
<br />
- Sarah contacted Cristian, who works in Cambridge and she will provide more information. One option is to provide JBrowse tracks.<br />
<br />
== IWM 2023 ==<br />
* Who is going?<br />
<br />
== Alliance/Caltech Literature ==<br />
* Caltech created a parallel PubMed search pipeline and paper editor UI for WormBase Parasite<br />
* Is this still being used?<br />
<br />
== Grants for AI/ML Readiness of Data ==<br />
* [https://grants.nih.gov/grants/guide/notice-files/not-od-23-082.html NOT-OD-23-082- Administrative Supplements to Support Collaborations to Improve the AI/ML-Readiness of NIH-Supported Data]<br />
* Proposal(s) from WB?<br />
<br />
== Bob Waterston single cell data ==<br />
* Data on staging<br />
* Bob said it looks great - also shared with his lab and John Murray <br />
* He asks if i)use log scale ii)display above CenGen and iii) if we want the L2 dataset from the 2017 paper in a similar format</div>Pnuinhttps://wiki.wormbase.org/index.php?title=WBConfCall_2021.03.18-Agenda_and_Minutes&diff=36497WBConfCall 2021.03.18-Agenda and Minutes2021-03-18T16:01:38Z<p>Pnuin: /* Metrics page prototype */</p>
<hr />
<div>= Help Desk =<br />
<br />
<br />
<br />
= Agenda and Minutes=<br />
* <br />
<br />
== Data migration to AGR conclusion ==<br />
Most - but not all - scientific data is held in AceDB<br />
We also hold "curation data", for example the curation status of a paper, separately<br />
How to transfer data is not yet urgent to sort out, as AGR has not yet created the DBs to transfer the data to. But it is good that we have awareness about which data is held where, and in which format, so we can scope and plan the work of incrementally transfer more and more data to the Alliance.<br />
<br />
==BioLink ML model example ==<br />
Circulated https://docs.google.com/presentation/d/1Kn7-zNhfZ9zo7bi3v3rSYDZrjJd_Vtq-aGGfH1Fk5YY/edit#slide=id.gc605ccf066_0_210<br />
Discussions around how the BioLink model could work for us, and how it could be implemented in different types of databases.<br />
<br />
== WB Paper Data to Alliance ==<br />
* Should we migrate our entire bibliography or only a subset?<br />
** Migrate a subset of papers for a defined list of species?<br />
** Some non-C. elegans papers may have been used as evidence for certain data types<br />
** Some of our non-C. elegans papers may be included in other groups' corpora<br />
* Some possible changes to WB models to improve our paper, author, person curation pipelines<br />
** Review ?Author model and create author ids<br />
** Would allow us to store author information from the PubMed XML in a more systematic way<br />
** Easier author-person curation, e.g. if we capture an author orcid from the PubMed XML, it would be easier to connect the right WBPerson<br />
** Retire #Affiliation hash and capture author information in a new ?Author model<br />
** Example In ACeDB<br />
[[File:Author_class_example.png]]<br />
<br />
<br />
Decision: We decide to share our entire bibliography to the Alliance.<br />
<br />
== Updated release letter ==<br />
Hx are thinking of reformatting the release letter<br />
<br />
== Upcoming WB Webinars ==<br />
<br />
<br />
== Cengen-de web app online ==<br />
<br />
<br />
== IWM 2021 WB workshop ==<br />
<br />
<br />
== WB annual/biannual publication in Genetics (in lieu of NAR) ==</div>Pnuinhttps://wiki.wormbase.org/index.php?title=WBConfCall_2021.03.18-Agenda_and_Minutes&diff=36490WBConfCall 2021.03.18-Agenda and Minutes2021-03-17T20:12:18Z<p>Pnuin: </p>
<hr />
<div>= Help Desk =<br />
<br />
<br />
<br />
= Agenda and Minutes=<br />
* <br />
<br />
== Data migration to AGR conclusion ==<br />
Most - but not all - scientific data is held in AceDB<br />
We also hold "curation data", for example the curation status of a paper, separately<br />
How to transfer data is not yet urgent to sort out, as AGR has not yet created the DBs to transfer the data to. But it is good that we have awareness about which data is held where, and in which format, so we can scope and plan the work of incrementally transfer more and more data to the Alliance.<br />
<br />
==BioLink ML model example ==<br />
Circulated https://docs.google.com/presentation/d/1Kn7-zNhfZ9zo7bi3v3rSYDZrjJd_Vtq-aGGfH1Fk5YY/edit#slide=id.gc605ccf066_0_210<br />
<br />
== WB Paper Data to Alliance ==<br />
* Should we migrate our entire bibliography or only a subset?<br />
** Migrate a subset of papers for a defined list of species?<br />
** Some non-C. elegans papers may have been used as evidence for certain data types<br />
** Some of our non-C. elegans papers may be included in other groups' corpora<br />
* Some possible changes to WB models to improve our paper, author, person curation pipelines<br />
** Review ?Author model and create author ids<br />
** Would allow us to store author information from the PubMed XML in a more systematic way<br />
** Easier author-person curation, e.g. if we capture an author orcid from the PubMed XML, it would be easier to connect the right WBPerson<br />
** Retire #Affiliation hash and capture author information in a new ?Author model<br />
<br />
<br />
== Upcoming WB Webinars ==<br />
<br />
<br />
== Cengen-de web app online ==<br />
<br />
<br />
== IWM 2021 WB workshop ==<br />
<br />
<br />
== WB annual/biannual publication in Genetics (in lieu of NAR) ==<br />
<br />
== Metrics page prototype ==</div>Pnuinhttps://wiki.wormbase.org/index.php?title=Tutorial:WormMine&diff=34247Tutorial:WormMine2019-07-14T00:28:40Z<p>Pnuin: /* WormMine Tutorial */</p>
<hr />
<div><br />
== WormMine Tutorial ==<br />
Links below explain in detail different aspects of the WormMine webpage, queries and results. They work like a small tour of the functionalities of the databases, while offering a small glimpse of the querying power of WormMine.<br />
<br />
[[Data Model]]<br />
<br />
[[Searching WormMine]]<br />
<br />
[[Lists]]<br />
<br />
[[Query Builder]]<br />
<br />
[[Query Results]]</div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:Table_7.png&diff=33615File:Table 7.png2018-11-15T17:59:19Z<p>Pnuin: Pnuin uploaded a new version of File:Table 7.png</p>
<hr />
<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:Querybuilder_5.png&diff=33614File:Querybuilder 5.png2018-11-15T17:53:29Z<p>Pnuin: Pnuin uploaded a new version of File:Querybuilder 5.png</p>
<hr />
<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:Querybuilder_4.png&diff=33612File:Querybuilder 4.png2018-11-15T17:47:26Z<p>Pnuin: Pnuin uploaded a new version of File:Querybuilder 4.png</p>
<hr />
<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:Querybuilder_3.png&diff=33611File:Querybuilder 3.png2018-11-15T17:44:30Z<p>Pnuin: Pnuin uploaded a new version of File:Querybuilder 3.png</p>
<hr />
<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:Querybuilder_2.png&diff=33610File:Querybuilder 2.png2018-11-15T17:41:33Z<p>Pnuin: Pnuin uploaded a new version of File:Querybuilder 2.png</p>
<hr />
<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=Searching_WormMine&diff=33557Searching WormMine2018-11-12T23:09:28Z<p>Pnuin: </p>
<hr />
<div><br />
=== Simple Search ===<br />
<br />
There are two simple search boxes on WormMine's home page, one on the right of the tab bar and one just below it. Both boxes generate similar results and any term can be searched, such as:<br />
<br />
* WormBase gene IDs, i.e. WBGene00000001</li><br />
* Sequence ID, i.e. Y110A7A.10</li><br />
* CDS Id, i.e. CDS:Y110A7A.10</li><br />
* Gene symbol, i.e. aap-1</li><br />
* GO term IDs, i.e. GO:000001</li><br />
* Keywords, i.e. kinase, homeobox</li><br />
<br />
[[File:simple_search_1.png]]<br />
<br />
Boolean searches ('''AND''', '''OR''', '''AND NOT''', etc., all caps) and wildcards ('''*''') are also available for some search terms, i.e. '''encodes AND homeobox''', '''worm AND NOT embryo''', '''kin*''', among other possibilities.<br />
<br />
<br />
The result page will display all items related to the term searched, be it a gene, a CDS, a transcript, a protein, etc, and most of the links will lead to a WormBase main site pages for a more detailed perspective on the item.<br />
<br />
<br />
[[File:simple_search_result_1.png]]<br />
<br />
===Templates===<br />
<br />
Templates in WormMine are curated and pre-defined queries that represent some of the most usual searches performed in the site. Templates are the easiest way to obtain a large amount of information in WormMine, fast. At the moment there are 25 unique templates available in WormMine, providing well-structure queries for genes, proteins, chromosomes and other ''C. elegans'' genomic elements, strains, phenotypes, etc.<br />
<br />
To run a template just click on the link in the index page and a page with options will be presented.<br />
<br />
[[File:template_1.png]]<br />
<br />
<br />
Select the desired query by clicking on it.<br />
<br />
<br />
[[File:template_2.png]]<br />
<br />
<br />
You can either modify some of the terms, constraints, etc and by clicking on <i>Show Results</i> will provide the results of the query in table format (how to manipulate this table can be found on the [[Query Results]] page)<br />
<br />
<br />
[[File:template_3.png]]<br />
<br />
<br />
[[File:template_4.png]]</div>Pnuinhttps://wiki.wormbase.org/index.php?title=Searching_WormMine&diff=33556Searching WormMine2018-11-12T23:06:19Z<p>Pnuin: </p>
<hr />
<div><br />
=== Simple Search ===<br />
<br />
There are two simple search boxes on WormMine's home page, one on the right of the tab bar and one just below it. Both boxes generate similar results and any term can be searched, such as:<br />
<br />
* WormBase gene IDs, i.e. WBGene00000001</li><br />
* Sequence ID, i.e. Y110A7A.10</li><br />
* CDS Id, i.e. CDS:Y110A7A.10</li><br />
* Gene symbol, i.e. aap-1</li><br />
* GO term IDs, i.e. GO:000001</li><br />
* Keywords, i.e. kinase, homeobox</li><br />
<br />
[[File:simple_search_1.png]]<br />
<br />
Boolean searches ('''AND''', '''OR''', '''AND NOT''', etc., all caps) and wildcards ('''*''') are also available for some search terms, i.e. '''encodes AND homeobox''', '''worm AND NOT embryo''', '''kin*''', among other possibilities.<br />
<br />
<br />
The result page will display all items related to the term searched, be it a gene, a CDS, a transcript, a protein, etc, and most of the links will lead to a WormBase main site pages for a more detailed perspective on the item.<br />
<br />
<br />
[[File:simple_search_result_1.png]]<br />
<br />
===Templates===<br />
<br />
Templates in WormMine are curated and pre-defined queries that represent some of the most usual searches performed in the site. Templates are the easiest way to obtain a large amount of information in WormMine, fast. At the moment there are 25 unique templates available in WormMine, providing well-structure queries for genes, proteins, chromosomes and other ''C. elegans'' genomic elements, strains, phenotypes, etc.<br />
<br />
To run a template just click on the link in the index page and a page with options will be presented.<br />
<br />
[[File:template_1.png]]<br />
<br />
<br />
Select the desired query by clicking on it.<br />
<br />
<br />
[[File:template_2.png]]<br />
<br />
<br />
You can either modify some of the terms, constraints, etc and by clicking on <i>Show Results</i> will provide the results of the query in table format (how to manipulate this table can be found on the [[Query Results]] page)<br />
<br />
<br />
[[File:template_3.png"]]<br />
<br />
<br />
[[File:template_4.png]]</div>Pnuinhttps://wiki.wormbase.org/index.php?title=Query_Results&diff=33555Query Results2018-11-12T22:52:20Z<p>Pnuin: </p>
<hr />
<div>==WormMine Results Page==<br />
<br />
===Results Page table===<br />
<br />
All WormMine query results are presented as tables. The number of resulting items is dependent on the query performed (number of rows) and the[[Data Model]] classes selected (number of columns, templates have a pre-defined set of columns). Most items in the table showed in blue are active links to WormBase pages, where more information about the item can be found. Hovering over the item will display a popup with a some summary information about it.<br />
<br />
<br />
[[File:results_1.png]] [[File:results_2.png]]<br />
<br />
<br />
<br />
===Column features===<br />
<br />
Results table have a small toolbox available in each column that allows for some operations to be performed<br />
<br />
[[File:images/toolbox.png]]<br />
<br />
<br />
* [[File:up_down.png]] up and down arrows allow for sorting, ascending and descending<br />
*[[File:x.png]] x allows the column to be removed<br />
*[[File:dotdotdot.png]] three dots toggle on and off the visibility of the column (it becomes an arrow when the columns is invisible [[File:arrow.png]])<br />
*[[File:funnel.png]] funnel acts as a filter selector that can be added or removed from the table. Multiple filters can be functional at the same time in different columns<br />
*[[File:bar_graph.png]] bar graph presents statistics about the column, at the same time that allows for filters to be added<br />
<br />
===Table manipulation===<br />
<br />
Results table also have a set of buttons, on top of the table, that provide some functionality on the results and also on exporting, saving and displaying contents. Some of these buttons open a dialog on top of the column with actions that can be performed and need to be dismissed to return to the result table.<br />
<br />
[[File:table_1.png]]<br />
<br />
<br />
*'''Manage Columns''' - allows the user to select column order, add and remove columns, add new columns that are not part of the query/template and sort the order of all columns in bulk [[File:table_2.png]]<br />
<br />
*'''Manage filters''' - allows for multiple filter management at once, including constraints and filter logic. The dialog allows to include filters from fields and items that are not part of the query/template [[File:table_3.png]]<br />
<br />
*'''Manage relationships''' - this works on excluding classes from the final result set, or making connections that are displayed in the results table to be optional on the screen, making related classes to appear nested (by using this feature a Undo button will the toggled on) [[File:table_4.png]]<br />
<br />
*'''Save as List''' - this button creates a list that can be saved by the user so it can be applied later on a different query or to be kept between releases, allowing for differences to be examined. One or multiple columns and rows can be selected, and a name has to be provided (to take full advantage, create an account and login first) [[File:table_5.png]]<br />
<br />
*'''Generate Code''' - query can be saved in multiple types of programming languages that take advantage of WormMine's API. Python, Perl, Java, Ruby, Javascript and XML are available [[File:table_6.png]]<br />
<br />
*'''Export''' - saves a text file with the items in the table. Columns and rows can be selected, headers can be added, at the same time as compression (useful for really long tables). Possibility of sending the results to a Galaxy or Genomespace service is available. Depending on the kind of results displayed, there are options to save the file as FASTA or other common formats [[File:table_7.png]]</div>Pnuinhttps://wiki.wormbase.org/index.php?title=Query_Results&diff=33554Query Results2018-11-12T22:49:25Z<p>Pnuin: </p>
<hr />
<div>==WormMine Results Page==<br />
<br />
===Results Page table===<br />
<br />
All WormMine query results are presented as tables. The number of resulting items is dependent on the query performed (number of rows) and the[[Data Model]] classes selected (number of columns, templates have a pre-defined set of columns). Most items in the table showed in blue are active links to WormBase pages, where more information about the item can be found. Hovering over the item will display a popup with a some summary information about it.<br />
<br />
<br />
[[File:results_1.png]] [[File:results_2.png]]<br />
<br />
<br />
<br />
===Column features===<br />
<br />
Results table have a small toolbox available in each column that allows for some operations to be performed<br />
<br />
[[File:images/toolbox.png]]<br />
<br />
<br />
* [[File:up_down.png]] up and down arrows allow for sorting, ascending and descending<br />
*[[File:x.png]] x allows the column to be removed<br />
*[[File:dotdotdot.png]] three dots toggle on and off the visibility of the column (it becomes an arrow when the columns is invisible [[File:arrow.png]])<br />
*[[File:funnel.png]] funnel acts as a filter selector that can be added or removed from the table. Multiple filters can be functional at the same time in different columns<br />
*[[File:bar_graph.png]] bar graph presents statistics about the column, at the same time that allows for filters to be added<br />
<br />
===Table manipulation===<br />
<br />
Results table also have a set of buttons, on top of the table, that provide some functionality on the results and also on exporting, saving and displaying contents. Some of these buttons open a dialog on top of the column with actions that can be performed and need to be dismissed to return to the result table.<br />
<br />
[[File:table_1.png]]<br />
<br />
<br />
*'''Manage Columns''' - allows the user to select column order, add and remove columns, add new columns that are not part of the query/template and sort the order of all columns in bulk [[File:table_2.png]]<br />
<br />
*'''Manage filters''' - allows for multiple filter management at once, including constraints and filter logic. The dialog allows to include filters from fields and items that are not part of the query/template [[File:table_3.png]]<br />
<br />
*'''Manage relationships''' - this works on excluding classes from the final result set, or making connections that are displayed in the results table to be optional on the screen, making related classes to appear nested (by using this feature a Undo button will the toggled on) [[File:table_4.png]]<br />
<br />
*'''Save as List''' - this button creates a list that can be saved by the user so it can be applied later on a different query or to be kept between releases, allowing for differences to be examined. One or multiple columns and rows can be selected, and a name has to be provided (to take full advantage, create an account and login first) [[File:table_5.png]]<br />
<br />
*'''Generate Code''' - query can be saved in multiple types of programming languages that take advantage of WormMine's API. Python, Perl, Java, Ruby, Javascript and XML are available [[File:table_6.png]]<br />
<br />
<li><b>Export</b> - saves a text file with the items in the table. Columns and rows can be selected, headers can be added, at the same time as compression (useful for really long tables). Possibility of sending the results to a Galaxy or Genomespace service is available. Depending on the kind of results displayed, there are options to save the file as FASTA or other commong formats.</li><br />
<img src="images/table_7.png" alt="table_1"></div>Pnuinhttps://wiki.wormbase.org/index.php?title=Query_Results&diff=33553Query Results2018-11-12T22:48:01Z<p>Pnuin: </p>
<hr />
<div>==WormMine Results Page==<br />
<br />
===Results Page table===<br />
<br />
All WormMine query results are presented as tables. The number of resulting items is dependent on the query performed (number of rows) and the[[Data Model]] classes selected (number of columns, templates have a pre-defined set of columns). Most items in the table showed in blue are active links to WormBase pages, where more information about the item can be found. Hovering over the item will display a popup with a some summary information about it.<br />
<br />
<br />
[[File:results_1.png]] [[File:results_2.png]]<br />
<br />
<br />
<br />
===Column features===<br />
<br />
Results table have a small toolbox available in each column that allows for some operations to be performed<br />
<br />
[[File:images/toolbox.png]]<br />
<br />
<br />
* [[File:up_down.png]] up and down arrows allow for sorting, ascending and descending<br />
*[[File:x.png]] x allows the column to be removed<br />
*[[File:dotdotdot.png]] three dots toggle on and off the visibility of the column (it becomes an arrow when the columns is invisible [[File:arrow.png]])<br />
*[[File:funnel.png]] funnel acts as a filter selector that can be added or removed from the table. Multiple filters can be functional at the same time in different columns<br />
*[[File:bar_graph.png]] bar graph presents statistics about the column, at the same time that allows for filters to be added<br />
<br />
===Table manipulation===<br />
<br />
Results table also have a set of buttons, on top of the table, that provide some functionality on the results and also on exporting, saving and displaying contents. Some of these buttons open a dialog on top of the column with actions that can be performed and need to be dismissed to return to the result table.<br />
<br />
[[File:table_1.png]]<br />
<br />
<br />
*'''Manage Columns''' - allows the user to select column order, add and remove columns, add new columns that are not part of the query/template and sort the order of all columns in bulk [[File:table_2.png]]<br />
<br />
*'''Manage filters''' - allows for multiple filter management at once, including constraints and filter logic. The dialog allows to include filters from fields and items that are not part of the query/template [[File:table_3.png]]<br />
<br />
*'''Manage relationships''' - this works on excluding classes from the final result set, or making connections that are displayed in the results table to be optional on the screen, making related classes to appear nested (by using this feature a Undo button will the toggled on) [[File:table_4.png]]<br />
<br />
<br />
<br />
<li><b>Save as List</b> - this button creates a list that can be saved by the user so it can be applied later on a different query or to be kept between releases, allowing for differences to be examined. One or multiple columns and rows can be selected, and a name has to be provided (to take full advantage, create an account and login first)</li><br />
<img src="images/table_5.png" alt="table_1"><br />
<li><b>Generate Code</b> - query can be saved in multiple types of programming languages that take advantage of WormMine's API. Python, Perl, Java, Ruby, Javascript and XML are available</li><br />
<img src="images/table_6.png" alt="table_1"><br />
<li><b>Export</b> - saves a text file with the items in the table. Columns and rows can be selected, headers can be added, at the same time as compression (useful for really long tables). Possibility of sending the results to a Galaxy or Genomespace service is available. Depending on the kind of results displayed, there are options to save the file as FASTA or other commong formats.</li><br />
<img src="images/table_7.png" alt="table_1"></div>Pnuinhttps://wiki.wormbase.org/index.php?title=Query_Results&diff=33552Query Results2018-11-12T22:45:26Z<p>Pnuin: </p>
<hr />
<div>==WormMine Results Page==<br />
<br />
===Results Page table===<br />
<br />
All WormMine query results are presented as tables. The number of resulting items is dependent on the query performed (number of rows) and the[[Data Model]] classes selected (number of columns, templates have a pre-defined set of columns). Most items in the table showed in blue are active links to WormBase pages, where more information about the item can be found. Hovering over the item will display a popup with a some summary information about it.<br />
<br />
<br />
[[File:results_1.png]] [[File:results_2.png]]<br />
<br />
<br />
<br />
===Column features===<br />
<br />
Results table have a small toolbox available in each column that allows for some operations to be performed<br />
<br />
[[File:images/toolbox.png]]<br />
<br />
<br />
* [[File:up_down.png]] up and down arrows allow for sorting, ascending and descending<br />
*[[File:x.png]] x allows the column to be removed<br />
*[[File:dotdotdot.png]] three dots toggle on and off the visibility of the column (it becomes an arrow when the columns is invisible [[File:arrow.png]])<br />
*[[File:funnel.png]] funnel acts as a filter selector that can be added or removed from the table. Multiple filters can be functional at the same time in different columns<br />
*[[File:bar_graph.png]] bar graph presents statistics about the column, at the same time that allows for filters to be added<br />
<br />
===Table manipulation===<br />
<br />
Results table also have a set of buttons, on top of the table, that provide some functionality on the results and also on exporting, saving and displaying contents. Some of these buttons open a dialog on top of the column with actions that can be performed and need to be dismissed to return to the result table.<br />
<br />
[[File:table_1.png]]<br />
<br />
<br />
*'''Manage Columns''' - allows the user to select column order, add and remove columns, add new columns that are not part of the query/template and sort the order of all columns in bulk [[File:table_2.png]]<br />
<br />
<li><b>Manage filters</b> - allows for multiple filter management at once, including constraints and filter logic. The dialog allows to include filters from fields and items that are not part of the query/template. </li><br />
<img src="images/table_3.png" alt="table_1"><br />
<li><b>Manage relationships</b> - this works on excluding classes from the final result set, or making connections that are displayed in the results table to be optional on the screen, making related classes to appear nested (by using this feature a Undo button will the toggled on) </li><br />
<img src="images/table_4.png" alt="table_1"><br />
<li><b>Save as List</b> - this button creates a list that can be saved by the user so it can be applied later on a different query or to be kept between releases, allowing for differences to be examined. One or multiple columns and rows can be selected, and a name has to be provided (to take full advantage, create an account and login first)</li><br />
<img src="images/table_5.png" alt="table_1"><br />
<li><b>Generate Code</b> - query can be saved in multiple types of programming languages that take advantage of WormMine's API. Python, Perl, Java, Ruby, Javascript and XML are available</li><br />
<img src="images/table_6.png" alt="table_1"><br />
<li><b>Export</b> - saves a text file with the items in the table. Columns and rows can be selected, headers can be added, at the same time as compression (useful for really long tables). Possibility of sending the results to a Galaxy or Genomespace service is available. Depending on the kind of results displayed, there are options to save the file as FASTA or other commong formats.</li><br />
<img src="images/table_7.png" alt="table_1"></div>Pnuinhttps://wiki.wormbase.org/index.php?title=Query_Results&diff=33551Query Results2018-11-12T22:44:24Z<p>Pnuin: </p>
<hr />
<div>==WormMine Results Page==<br />
<br />
===Results Page table===<br />
<br />
All WormMine query results are presented as tables. The number of resulting items is dependent on the query performed (number of rows) and the[[Data Model]] classes selected (number of columns, templates have a pre-defined set of columns). Most items in the table showed in blue are active links to WormBase pages, where more information about the item can be found. Hovering over the item will display a popup with a some summary information about it.<br />
<br />
<br />
[[File:results_1.png]] [[File:results_2.png]]<br />
<br />
<br />
<br />
===Column features===<br />
<br />
Results table have a small toolbox available in each column that allows for some operations to be performed<br />
<br />
[[File:images/toolbox.png]]<br />
<br />
<br />
* [[File:up_down.png]] up and down arrows allow for sorting, ascending and descending<br />
*[[File:x.png]] x allows the column to be removed<br />
*[[File:dotdotdot.png]] three dots toggle on and off the visibility of the column (it becomes an arrow when the columns is invisible [[File:arrow.png]])<br />
*[[File:funnel.png]] funnel acts as a filter selector that can be added or removed from the table. Multiple filters can be functional at the same time in different columns<br />
*[[File:bar_graph.png]] bar graph presents statistics about the column, at the same time that allows for filters to be added<br />
<br />
===Table manipulation===<br />
<br />
Results table also have a set of buttons, on top of the table, that provide some functionality on the results and also on exporting, saving and displaying contents. Some of these buttons open a dialog on top of the column with actions that can be performed and need to be dismissed to return to the result table.<br />
<br />
[[File:table_1.png]]</div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:Funnel.png&diff=33550File:Funnel.png2018-11-12T22:42:40Z<p>Pnuin: </p>
<hr />
<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:Dotdotdot.png&diff=33549File:Dotdotdot.png2018-11-12T22:42:32Z<p>Pnuin: </p>
<hr />
<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:Bar_graph.png&diff=33548File:Bar graph.png2018-11-12T22:42:23Z<p>Pnuin: </p>
<hr />
<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:Arrow.png&diff=33547File:Arrow.png2018-11-12T22:42:14Z<p>Pnuin: </p>
<hr />
<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:Toolbox.png&diff=33546File:Toolbox.png2018-11-12T22:41:56Z<p>Pnuin: </p>
<hr />
<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:X.png&diff=33545File:X.png2018-11-12T22:41:44Z<p>Pnuin: </p>
<hr />
<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:Up_down.png&diff=33544File:Up down.png2018-11-12T22:41:34Z<p>Pnuin: </p>
<hr />
<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=Query_Results&diff=33543Query Results2018-11-12T22:41:21Z<p>Pnuin: </p>
<hr />
<div>==WormMine Results Page==<br />
<br />
===Results Page table===<br />
<br />
All WormMine query results are presented as tables. The number of resulting items is dependent on the query performed (number of rows) and the[[Data Model]] classes selected (number of columns, templates have a pre-defined set of columns). Most items in the table showed in blue are active links to WormBase pages, where more information about the item can be found. Hovering over the item will display a popup with a some summary information about it.<br />
<br />
<br />
[[File:results_1.png]] [[File:results_2.png]]<br />
<br />
<br />
<br />
===Column features===<br />
<br />
Results table have a small toolbox available in each column that allows for some operations to be performed<br />
<br />
[[File:images/toolbox.png]]<br />
<br />
<br />
* [[File:up_down.png]] up and down arrows allow for sorting, ascending and descending<br />
*[[File:x.png]] x allows the column to be removed<br />
*[[File:dotdotdot.png]] three dots toggle on and off the visibility of the column (it becomes an arrow when the columns is invisible [[File:arrow.png]])<br />
<li><img src="images/funnel.png" alt="funnel" width="15" height="21"> funnel acts as a filter selector that can be added or removed from the table. Multiple filters can be functional at the same time in different columns.</li><br />
<li><img src="images/bar_graph.png" alt="bar_graph" width="20" height="19"> bar graph presents statistics about the column, at the same time that allows for filters to be added</li></div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:Results_2.png&diff=33542File:Results 2.png2018-11-12T22:38:11Z<p>Pnuin: </p>
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<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:Results_1.png&diff=33541File:Results 1.png2018-11-12T22:37:57Z<p>Pnuin: </p>
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<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=Query_Results&diff=33540Query Results2018-11-12T22:37:37Z<p>Pnuin: Created page with "==WormMine Results Page== ===Results Page table=== All WormMine query results are presented as tables. The number of resulting items is dependent on the query performed..."</p>
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<div>==WormMine Results Page==<br />
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===Results Page table===<br />
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All WormMine query results are presented as tables. The number of resulting items is dependent on the query performed (number of rows) and the[[Data Model]] classes selected (number of columns, templates have a pre-defined set of columns). Most items in the table showed in blue are active links to WormBase pages, where more information about the item can be found. Hovering over the item will display a popup with a some summary information about it.<br />
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[[File:results_1.png]] [[File:results_2.png]]</div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:Table_8.png&diff=33539File:Table 8.png2018-11-12T22:35:47Z<p>Pnuin: </p>
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<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:Table_7.png&diff=33538File:Table 7.png2018-11-12T22:35:38Z<p>Pnuin: </p>
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<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:Table_6.png&diff=33537File:Table 6.png2018-11-12T22:35:27Z<p>Pnuin: </p>
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<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:Table_5.png&diff=33536File:Table 5.png2018-11-12T22:35:18Z<p>Pnuin: </p>
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<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:Table_4.png&diff=33535File:Table 4.png2018-11-12T22:35:04Z<p>Pnuin: </p>
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<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:Table_3.png&diff=33534File:Table 3.png2018-11-12T22:34:43Z<p>Pnuin: </p>
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<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:Table_2.png&diff=33533File:Table 2.png2018-11-12T22:34:30Z<p>Pnuin: </p>
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<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=File:Table_1.png&diff=33532File:Table 1.png2018-11-12T22:34:11Z<p>Pnuin: </p>
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<div></div>Pnuinhttps://wiki.wormbase.org/index.php?title=Query_Builder&diff=33531Query Builder2018-11-12T22:32:47Z<p>Pnuin: </p>
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<div>===WormMine QueryBuilder===<br />
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You can setup your own queries by using the QueryBuilder. The builder is a powerful tool that allows the user to create queries that can span different classes in WormMine and overall different sources of information. <br />
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The easiest way to get acquainted with the QueryBuilder is to edit and modify a template (just click on the ''Edit Query'' button [[File:querybuilder_1.png]]). The builder can be also accessed by clicking on the ''Select a Data Type to Begin a Query'' box from the QueryBuilder page, or by clicking the name of the class in the [[Data Model]]. By clicking on the class name, it will bring the builder interface shown below.<br />
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[[File:querybuilder_2.png]]<br />
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There are two options to add items from the Model Browser side of the screen to the query: <br />
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* Clicking on ''Show'' will transfer the item to the query and the result will have the items'information, meaning all elements with that item will be shown in the final table<br />
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[[File:querybuilder_3.png]]<br />
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* Clicking on ''Constrain'' will also transfer the item to query, but will ask for input regarding the constraint to be applied. If, for instance, Gene Name is selected, the dialog will ask for a match (=) or not (!=), or some other filter (boolean and wildcards accepted). The last piece of information is how the constrain join will be applied, where the filter will either '''HAVE''' or '''NOT''' a value. Take a look at the image below.<br />
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[[File:querybuilder_4.png]]<br />
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Adding the constraint to the query will have it displayed on the right side of the screen. We can add more constraints, that will filter even more the result and we can add more <i>Show</i> items, what will included additional columns to the result table. <br />
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[[File:querybuilder_5.png]]<br />
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The columns to be displayed are shown at the bottom of the builder. Column order can be easily modified by dragging and dropping the boxes in the desired order. To run the query, simply click on ''Show Results'' [[File:querybuilder_7.png]].<br />
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[[File:querybuilder_6.png]]</div>Pnuinhttps://wiki.wormbase.org/index.php?title=Query_Builder&diff=33530Query Builder2018-11-12T22:31:16Z<p>Pnuin: </p>
<hr />
<div>===WormMine QueryBuilder===<br />
<br />
You can setup your own queries by using the QueryBuilder. The builder is a powerful tool that allows the user to create queries that can span different classes in WormMine and overall different sources of information. <br />
<br />
<br />
The easiest way to get acquainted with the QueryBuilder is to edit and modify a template (just click on the ''Edit Query'' button [[File:querybuilder_1.png]]). The builder can be also accessed by clicking on the ''Select a Data Type to Begin a Query'' box from the QueryBuilder page, or by clicking the name of the class in the [[Data Model]]. By clicking on the class name, it will bring the builder interface shown below.<br />
<br />
<br />
[[File:querybuilder_2.png]]<br />
<br />
There are two options to add items from the Model Browser side of the screen to the query: <br />
<br />
* Clicking on ''Show'' will transfer the item to the query and the result will have the items'information, meaning all elements with that item will be shown in the final table<br />
<br />
<br />
[[File:querybuilder_3.png]]<br />
<br />
<br />
* Clicking on ''Constrain'' will also transfer the item to query, but will ask for input regarding the constraint to be applied. If, for instance, Gene Name is selected, the dialog will ask for a match (=) or not (!=), or some other filter (boolean and wildcards accepted). The last piece of information is how the constrain join will be applied, where the filter will either '''HAVE''' or '''NOT''' a value. Take a look at the image below.</div>Pnuinhttps://wiki.wormbase.org/index.php?title=Query_Builder&diff=33529Query Builder2018-11-12T22:26:04Z<p>Pnuin: </p>
<hr />
<div>===WormMine QueryBuilder===<br />
<br />
You can setup your own queries by using the QueryBuilder. The builder is a powerful tool that allows the user to create queries that can span different classes in WormMine and overall different sources of information. <br />
<br />
<br />
The easiest way to get acquainted with the QueryBuilder is to edit and modify a template (just click on the ''Edit Query'' button [[File:querybuilder_1.png]]). The builder can be also accessed by clicking on the ''Select a Data Type to Begin a Query'' box from the QueryBuilder page, or by clicking the name of the class in the [[Data Model]]. By clicking on the class name, it will bring the builder interface shown below.</div>Pnuin