Difference between revisions of "Phenotype micropublications"

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The underlying CGI will remain the same but the Allele-phenotype and the Phenotype-micropublications form will have 2 separate displays.
 
The underlying CGI will remain the same but the Allele-phenotype and the Phenotype-micropublications form will have 2 separate displays.
  
==Changes to the form==
+
==General==
  
 
* please note, if users are accessing the from through the 'Submit data' button on WormBase they should be asked:
 
* please note, if users are accessing the from through the 'Submit data' button on WormBase they should be asked:
Line 8: Line 8:
 
'I am submitting novel results'.
 
'I am submitting novel results'.
  
Those should be 2 different buttons. If they click on 'I am submitting published results' they will be directed to the current allele-phenotype form
+
Those should be 2 different buttons. If they click on 'I am submitting published results' they will be directed to the current allele-phenotype form.
 +
 
 
if they click on 'I am submitting novel results'
 
if they click on 'I am submitting novel results'
 
they will be redirected to the allele-micropublication from
 
they will be redirected to the allele-micropublication from
  
Changes to the current Allele-phenotype form located here: http://www.wormbase.org/submissions/phenotype.cgi:
+
==Changes to the form==
 +
 
 +
Changes to the current Allele-phenotype form located here: http://www.wormbase.org/submissions/phenotype.cgi
 +
the '''phenotype micropublicaton form''' is here:
 +
http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_micropub.cgi
 +
 
 
Expression micropublication form here: http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/expr_micropub.cgi
 
Expression micropublication form here: http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/expr_micropub.cgi
  
Line 22: Line 28:
 
Change the descriptive text at the beginning with:
 
Change the descriptive text at the beginning with:
  
'If you have unpublished phenotype data you can micropublish it on WormBase by filling the form below. The form is mostly self explanatory and hints can be found by clicking green question marks. In the box on the right side of the page you can find additional tips/information that will appear when you start typing in specific fields. Should you have additional questions you can find guidelines here.'
+
'If you have unpublished phenotype data you can micropublish it on WormBase by filling the form below. The form is mostly self explanatory and hints can be found by clicking green question marks. In the box on the right side of the page you can find additional tips/information that will appear when you start typing in specific fields.'
  
 
Remove:
 
Remove:
Line 34: Line 40:
 
* Laboratory -> autocomplete on labs  -> mandatory
 
* Laboratory -> autocomplete on labs  -> mandatory
 
* Funding -> free text  -> mandatory
 
* Funding -> free text  -> mandatory
* Species -> autocomplete on species?
+
* Species -> autocomplete on species? -> mandatory
 
* Choose an image -> Browse button, only jpg accepted  -> mandatory
 
* Choose an image -> Browse button, only jpg accepted  -> mandatory
* Description -> big text (small box that becomes big upon clicking)
+
* Description -> big text (small box that becomes big upon clicking) -> mandatory
  
The change below for genetic perturbations could be a generic change to the form -> to discuss with Chris
 
 
Change:
 
Change:
 
* Genetic perturbation(s) in -> Perturbation(s)
 
* Genetic perturbation(s) in -> Perturbation(s)
* this text: 'PLEASE NOTE: All genetic perturbations above will be annotated to all phenotypes entered below. For separate perturbation-phenotype annotations, please perform separate submissions, or use the WormBase Phenotype Worksheet (linked above).'  
+
* this text: 'PLEASE NOTE: All genetic perturbations above will be annotated to all phenotypes entered below. For separate perturbation-phenotype annotations, please perform separate submissions.'  
  
in this: 'PLEASE NOTE: All perturbations above will be annotated to all phenotypes entered below. For separate perturbation-phenotype annotations, please perform separate submissions, or use the WormBase Phenotype Worksheet (linked above).'
+
in this: 'PLEASE NOTE: All perturbations above will be annotated to all phenotypes entered below. For separate perturbation-phenotype annotations, please perform separate submissions.'
  
 
Add -below 'Transgene' field:
 
Add -below 'Transgene' field:
 
Molecule -> autocomplete on molecules
 
Molecule -> autocomplete on molecules
  
Add Section called "Article details" -above 'Optional' section (see http://www.wormbase.org/submissions/expr_micropub.cgi)
+
* In the phenotype field, get rid of Personal communication
* Description of results -> large free text box
+
* get rid of phenotype remark
* Title of the Submission -> free text box
+
 
 +
Add Section called "Publication details" -above 'Optional' section (see http://www.wormbase.org/submissions/expr_micropub.cgi)
 +
* Title of the Submission -> free text box -> Mandatory
 
* Suggested Reviewer ->free text box
 
* Suggested Reviewer ->free text box
 
* Comments to editors -> free text box
 
* Comments to editors -> free text box
Line 80: Line 87:
  
 
What is listed as figure legend 1 should go into reagents- also other tech notes do not have the caption but only the descriptive text
 
What is listed as figure legend 1 should go into reagents- also other tech notes do not have the caption but only the descriptive text
 +
 +
 +
===current form functionality (August 2017)===
 +
<pre>
 +
Phenotype micropublication:
 +
If RNAi causes the phenotype:
 +
When entering values in the RNAi field:
 +
-an object is generated in RNAi OA capturing
 +
— phenotype observed or not observed
 +
— no dump tag
 +
— needs review tag
 +
— community curator tag
 +
— DNA text (what goes into the RNAi field in from)
 +
— Species
 +
 +
Image is saved
 +
 +
DOES NOT collect in OA:
 +
— ORCID
 +
— Coauthors
 +
— Lab
 +
— Funding
 +
— Main text of micro
 +
— Title of the submission
 +
— Suggested reviewer
 +
— comments to editors
 +
— References
 +
 +
 +
If allele causes the phenotype:
 +
-an object is generated in phenotype OA capturing
 +
— phenotype observed or not observed
 +
— variation
 +
— no dump tag
 +
— needs review tag
 +
— community curator tag
 +
 +
Image is saved
 +
 +
DOES NOT collect in OA:
 +
— ORCID
 +
— Coauthors
 +
— Lab
 +
— Funding
 +
— Main text of micro
 +
— Title of the submission
 +
— Suggested reviewer
 +
— comments to editors
 +
— References
 +
 +
 +
If transgene causes the phenotype:
 +
-an object is generated in phenotype OA capturing
 +
— phenotype observed or not observed
 +
— transgene
 +
— caused by other (gene causing the phenotype)
 +
— no dump tag
 +
— needs review tag
 +
— community curator tag
 +
 +
Image is saved
 +
 +
DOES NOT collect in OA:
 +
— ORCID
 +
— Coauthors
 +
— Lab
 +
— Funding
 +
— Main text of micro
 +
— Title of the submission
 +
— Suggested reviewer
 +
— comments to editors
 +
— References
 +
 +
If molecule causes the phenotype:
 +
No object is generated in OA
 +
 +
Image is saved
 +
 +
</pre>

Latest revision as of 18:29, 16 August 2017

For Phenotype-micropublications submissions we will modify the existing Allele-phenotype submission form. The underlying CGI will remain the same but the Allele-phenotype and the Phenotype-micropublications form will have 2 separate displays.

General

  • please note, if users are accessing the from through the 'Submit data' button on WormBase they should be asked:

'I am submitting published results' 'I am submitting novel results'.

Those should be 2 different buttons. If they click on 'I am submitting published results' they will be directed to the current allele-phenotype form.

if they click on 'I am submitting novel results' they will be redirected to the allele-micropublication from

Changes to the form

Changes to the current Allele-phenotype form located here: http://www.wormbase.org/submissions/phenotype.cgi the phenotype micropublicaton form is here: http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/phenotype_micropub.cgi

Expression micropublication form here: http://mangolassi.caltech.edu/~azurebrd/cgi-bin/forms/expr_micropub.cgi

Change this title Contribute phenotype connections to WormBase into Micropublish phenotype results!

Change the descriptive text at the beginning with:

'If you have unpublished phenotype data you can micropublish it on WormBase by filling the form below. The form is mostly self explanatory and hints can be found by clicking green question marks. In the box on the right side of the page you can find additional tips/information that will appear when you start typing in specific fields.'

Remove:

  • PubMedID -submissions are novel data, do not have a paper attached. Submissions will get their own WBPaperID
  • Click here to review your publications and see which are in need of phenotype curation -this field not necessary in the micropublication form

Add ORCID field below 'Your Name' field

Add -below 'Your e-mail address' field:

  • co-authors -> autocomplete on people
  • Laboratory -> autocomplete on labs -> mandatory
  • Funding -> free text -> mandatory
  • Species -> autocomplete on species? -> mandatory
  • Choose an image -> Browse button, only jpg accepted -> mandatory
  • Description -> big text (small box that becomes big upon clicking) -> mandatory

Change:

  • Genetic perturbation(s) in -> Perturbation(s)
  • this text: 'PLEASE NOTE: All genetic perturbations above will be annotated to all phenotypes entered below. For separate perturbation-phenotype annotations, please perform separate submissions.'

in this: 'PLEASE NOTE: All perturbations above will be annotated to all phenotypes entered below. For separate perturbation-phenotype annotations, please perform separate submissions.'

Add -below 'Transgene' field: Molecule -> autocomplete on molecules

  • In the phenotype field, get rid of Personal communication
  • get rid of phenotype remark

Add Section called "Publication details" -above 'Optional' section (see http://www.wormbase.org/submissions/expr_micropub.cgi)

  • Title of the Submission -> free text box -> Mandatory
  • Suggested Reviewer ->free text box
  • Comments to editors -> free text box
  • References -> Field that allows PMID entries
  • Disclaimer -> mandatory checkbox like in the Expression micropublication form: I declare to the best of my knowledge that the experiment is reproducible.
Mockup.png

Changes to the OAs

Phenotype OA

Add a Picture field

Title?

Shall we add a 'Title' field or shall we autogenerate titles with the info that are entered in different fields?

Modelling Nemametrix data

Nema micro 1.png
Nema micro 2.png

notes

The strain is a model for human disease Can the annotation be to strain-phenotype?

No funding listed for this experiment on the nemametrix site Add: Funding: National Institute of Aging SBIR 1R43AG047020 to NemaMetrix Inc.

What is listed as figure legend 1 should go into reagents- also other tech notes do not have the caption but only the descriptive text


current form functionality (August 2017)

Phenotype micropublication:
If RNAi causes the phenotype:
When entering values in the RNAi field:
-an object is generated in RNAi OA capturing
— phenotype observed or not observed
— no dump tag
— needs review tag
— community curator tag
— DNA text (what goes into the RNAi field in from)
— Species

Image is saved 

DOES NOT collect in OA:
— ORCID
— Coauthors
— Lab
— Funding
— Main text of micro
— Title of the submission
— Suggested reviewer
— comments to editors
— References


If allele causes the phenotype:
-an object is generated in phenotype OA capturing
— phenotype observed or not observed
— variation
— no dump tag
— needs review tag
— community curator tag

Image is saved

DOES NOT collect in OA:
— ORCID
— Coauthors
— Lab
— Funding
— Main text of micro
— Title of the submission
— Suggested reviewer
— comments to editors
— References


If transgene causes the phenotype:
-an object is generated in phenotype OA capturing
— phenotype observed or not observed
— transgene
— caused by other (gene causing the phenotype)
— no dump tag
— needs review tag
— community curator tag

Image is saved

DOES NOT collect in OA:
— ORCID
— Coauthors
— Lab
— Funding
— Main text of micro
— Title of the submission
— Suggested reviewer
— comments to editors
— References

If molecule causes the phenotype:
No object is generated in OA

Image is saved