Phenote Fields

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Fields for curating using Phenote

Note: These fields were initially made for Carol for use in the Phenote annotator. We stopped using phenote in the beginning of 2010.
*” required (doesn’t pertain to NBP alleles)
Not dumped” information does not get loaded into the .ace file.

Tab 1 – Object entry, information retrieval

PgdbId

Not dumped. This is the Postgres database ID that records the action and is assigned automatically on “save data” and viewed upon ‘save data’ or object ‘retrieve’. This is in-house for Postgres only.

*Curation_status

Dropdown list for in-house paper-filing and counting. Use this to specify how ‘done’ you are with a paper. Although not part of the save constraint pipeline, if you do not choose a value, the paper will not be included in any status counts. The .obo file includes the values

happy” DEF: record is complete and the world loves us, XXOO
not_happy” DEF: the world loves us but we know better, xoo
down_right_disgusted” DEF: the world will hate us if we don’t’ fix this ASAP! ☹

*Curator

Enter the Curator from a dropdown list of all curators. Information is stored in an .obo file that reports data in the Term Info box. You can also enter by typing, selecting the text finishing options. Enter by choosing name from the list, or if typing in, by hitting return or clicking in new field.

*Object Type

Enter the type of object: Allele, Transgene, Rearrangement, Multi-allele from the dropdown list. Enter by choosing an object from the list, or if typing in, by hitting return or clicking in new field.

WS_current info

Object look-up field, use to verify that an allele or rearrangement exists in the database already. Enter object name and press retrieve to view information from the latest WS build. For alleles, the gene connection will be displayed if there is one. For rearrangements, the information retrieved includes the genes mapped inside and outside of the object. You need to retype the allele or rearrangement into the Object Name field.

*Object Name:

Enter object name by hitting return, moving to new field or retrieve. You must hit retrieve if you want to see Postgres information.

Allele. Verify allele identity by retrieving WS_current info for the allele. Re-enter the allele in this field. Hit retrieve to pull up all Postgres information.
Rearrangement. Verify rearrangement the same way as allele. Retrieve WS_current info for the rearrangement. If the rearrangement already exists as of the last build, the LG and genes inside the rearrangement will be displayed. Once verified, enter object in Object Name field. If rearrangement doesn’t already exist, it will be added to the Mary Ann’s list along with the other non-pre-existing alleles.
Transgene. First, verify the transgene by retrieving Pub info. The Pub retrieve will display all transgenes and summary information for the transgenes curated for that paper. This is mostly necessary when authors do not use standard nomenclature to name the transgene, in which case it is possible that Wen assigned a name to it, which we need to use. If a name hasn’t been assigned, the transgene will be added to a transgene verification form for Wen in a nightly cron job. For integrated transgenes, try to include, name, genotype, map position and integration means. For extrachromosomal arrays, include name and genotype. All notes on transgenes can be placed in the Object remark field. NOTE: Wen is pretty much caught up on integrated transgenes and we will therefore most likely not have to enter info about them. On the other hand, she has not curated Ex arrays, so this may be a large class of objects we will have to work with her to create.
Multi-allele. This sub-class was initially implemented for capturing interaction data. We need to ‘suppress’(?) this data until the interaction model is up and running and then migrate it over to the new model. Currently it is not on the Object_type list.
If there is no information in the database for the variation object or transgene, on commit, the object will be sent to 
the respective curators for verification, that is, new alleles will be posted to the object-verification form for Mary Ann
and new transgenes will be posted for Wen.

*Pub

Publication entry. Text-finishing field based on a publication .obo file. Can enter publication based on Title or WBPaperID number. Will get an “error” message when hitting paper retrieve if no allele/phenotype has been entered into Postgres linked to that paper yet and therefore no records can be retrieved.

Use this field to retrieve transgenes for a paper to verify the object name for those transgenes that do not use standard nomenclature.

*Person

Text-finishing field based on person .obo file. Start entering name, First, Middle or Last and choose the person. .obo file to the right shows specific information for eyeball validation.

Paper Remark

Not dumped. Enter remarks that should be attached to all papers.

Paper Remark History

Read only concatenated remarks attached to all entries for one paper.

Object Remark: Not dumped, M.A. and W.

This is for conveying in-house curatorial information. This is viewed by Mary Ann and Wen and so can be used to store notes concerning allele and transgene genotypes or other summary information.

Allele Status: Not dumped, part of job for M.A.

Text field. Not dumped. Denote if the allele is an orphan or if the gene it is associated with has been lost or designated a different name in the paper. If this field is filled it should cause the allele and the information in this field to be displayed on Mary Ann’s allele verification form.

Tab 2 – Phenotype information

NOT

This should be a check box, for now it is a dropdown list of blank or checked, with a blank entry by default. Use when the phenotype has been demonstrated to be absent.

*Phenotype

Dropdown list from phenotype ontology .obo file, text finishing. Start typing a phenotype and you will be shown a list of possible terms, the information panel will show you the hierarchy as well as the WBPhenotypeID and definition etc. You can also select by synonym (pretty slick, i.e. Muv, but a bit cumbersome when the synonym is linked to many terms, i.e. let).

Phenotype Remark

This is a queryable text field. Use to clarify the assigned phenotype term.

Anatomy

Dropdown list from the anatomy ontology .obo (Raymond’s) file, text finishing. Start typing a term and you will be shown a list of possible terms, the information panel will show you the hierarchy as well as the WBbt:ID and definition etc. This field will also allow multiply entries. To delete a term, select it from the box and press delete.

Life Stage

Dropdown list from the life stage ontology .obo (Wen’s) file, text finishing. Start typing a term and you will be shown a list of possible terms, the information panel will show you the hierarchy as well as the WBls:ID and definition etc. This field will also allow multiply entries. To delete a term select it from the box and press delete.

EQ schema

the following fields are for the PATO EQ development. For now, do not worry about them.

Entity:
Quality: (PATO)]
Suggested: Text box for EQ term notes.

Allele Nature

Dropdown list from WBnature .obo file (created by J). Values are same as on CGI.

Functional Change

Dropdown list from WBfunc .obo file (created by J). Values are the same as on the CGI.

Temperature

Text. Degree symbol is not accepted by the .ace file so it is not necessary to add it. Text temp scale (C) is accepted, displayed in the .ace and migrated to acedb. We will need to request that these symbols are displayed on the website.

Treatment

Text. Use to report specifics of the experiment.


Tab 3 – Phenotype Information continued

Penetrance

Dropdown list from WBpenetrance .obo file. Values same as on CGI. “Complete no longer fills in “100” in Range fields.

Penetrance Remark

Queryable text field, for notes about changes in penetrance, or more recently, I add the value if only one penetrance value is reported.

Penetrance Range Start

Integer. Only enter if you have an ending range. If not then this starting number will be copied into the ending range field and the display will look silly.

Penetrance Range End

Integer.

Heat Sensitive

This should be a check box, now it is a dropdown list of nothing or checked.

Heat Sensitive Degree

Text field, but good to just enter integer.

Cold Sensitive

This should be a check box, now it is a dropdown list of nothing or checked.

Cold Sensitive Degree

Text field, but good to just enter integer.

Maternal effect

Dropdown list from WBmat_effect .obo file. Values the same as on CGI form.

Paternal effect

This should be a check box, now it is a dropdown list of nothing or checked.

Haplo

Haploinsufficiency, use only if authors present dosage effect results. This should be a check box, now it is a dropdown list of nothing or checked.

Tab 4 – Genotype/ Genetic Interaction/ NBP Data Curation Fields

Genotype

Enter background genotype of the animal whose phenotype you are reporting. For new transgenes, try to add as much information as possible; this information will go to Wen's object-verification form if the object is a new transgene.

Strain

On the CGI, this field required the correct CGC WB strain name. This is no longer a constraint. However; this form is not a strain entry form, the purpose of us curating strains is not entirely clear...to link the strain to the paper that reports phenotypic comments for it? Since CGC strains (which are the only ones that can be entered here) can be linked to papers via textpresso, and papers are linked to phenotypes, the path is already taken care of. The only non-redundant action would be to enter in strain names that don’t exist in the CGC, but this is of little value since they aren’t necessarily publicly available and when they are—the CGC will be entering the data themselves.

Genetic Intx Desc

Not dumped. In house text box, used to mark papers for interactions. Comments in one line will be carried over to all lines for that allele curated with the same reference source, the same way it worked on the CGI form, e.g. the interaction description is tied to all entries for an allele of a single paper.

NBP

Auto-filled phenotype data sent from Shohei Mitani's lab Japan via Sanger and curated here. NBP: National Bioresource Project.

NBP date

Use to query NBP data by date.

Lab

Use this field for phenotypes only reported by the NBP group, FX laboratory_name. If the NBP sends us comments from other labs, enter a WBPersonID in the Person field. Maintain a standard comment: “Comments relayed from the National Bioresource Project in Japan.” Still needs to be added to .ace dumper—cannot test this field until it is added.

Changes from Carol’s CGI

  • There is no automated WB dev site query for final name and gene association, this is now done by eyeballing term info from static lists updated from Citace after every new build through the WS_current field.
  • Curation_status takes the place of "paper_complete" and will be used to keep tally of the progress through the plethora of papers.
  • Data is no longer divided by "big box".
  • All drop down lists are in the form of .obo files.



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--kjy