Phenote Fields

IV. Phenote Fields “*” required (doesn’t pertain to NBP alleles) “Not dumped” information does not get loaded into the .ace file. 15:51, 13 March 2008 (EDT)~ Tab 1 – Object entry, information retrieval 15:51, 13 March 2008 (EDT)~ 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: Dropdown list, .obo file, text finishing.

• Object Type: Dropdown list of Allele, Transgene, Rearrangement, Multi-allele. Object_type entered by hitting return or clicking new field.

WS_current info: Allele look-up field. Enter allele and press retrieve to view information from the latest WS build about an allele. Use to verify allele details. If there is no information, a daily cron job will identify it and place it on an allelel-verification form for Mary Ann ( http://tazendra.caltech.edu/~Postgres/cgi-bin/new_objects.cgi ). You need to retype allele into 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 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.

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

• 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. This is for conveying in-house curatorial information. This is viewed by Mary Ann and so can be used to store notes concerning allele object or allele-gene connections, especially those that need to be created by her.

Allele Status (Orphan): Text field. Not dumped. Denote if the allele is an orphan or if the gene it is associated with has been lost. 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.

15:51, 13 March 2008 (EDT)~ Tab 2 – Phenotype information 15:51, 13 March 2008 (EDT)~ NOT: This should be check box, now it is a dropdown list of nothing or checked. Use when the phenotype has been demonstrated to be lacking by the animal.

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: ?text field. Use to clarify the assigned phenotype term. (It would be good if this box was bigger or auto-adjusted to fit content.)

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. (It would be good if this box was bigger or auto-adjusted to fit content.)

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. (It would be good if this box was bigger or auto-adjusted to fit content.)

[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).

Functional Change: Dropdown list from WBfunc .obo file (created by J).

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. (It would be good if this box was bigger or auto-adjusted to fit content.)

15:51, 13 March 2008 (EDT)~ Tab 3 – Phenotype Information continued 15:51, 13 March 2008 (EDT)~ Penetrance: Dropdown list from WBpenetrance .obo file. “Complete no longer fills in “100” in Range fields.

Penetrance Remark: ?text field, for notes about changes in penetrance, or more recently, I add the value if only one value is supplied.

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 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 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.

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

15:51, 13 March 2008 (EDT)~~ Tab 4 – Phenotype cont/ NBP data curation fields 15:51, 13 March 2008 (EDT)~~ Genotype: enter background genotype of animal whose phenotype you are reporting.

Strain: needs to be correct WB strain name. This 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 re-enter the data.

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 Japan via Sanger and processed here.

NBP date: Use to query NBP data by date.

Lab: .obo file for laboratory that reports the data. In this case always filled with FX for the NBP alleles. When NBP phenotype reports are actually from other people, put their name in the WBPersonID. Maintain standard comment that “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.

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