Biological process xp self ProgressNotesNov2008

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11th November

Jennifer Deegan

In a meeting today at the Editorial Office we figured out who will be responsible for which cross products file. I am responsible for the 'biological_process_xp_self' file.

I am to read through the file and check the biological content of the intersection tags. Any edits are to be made by hand in the file, but OBO-Edit2 is currently able to be used as a browser. Where specific domain knowledge is needed I can send list of terms to people who have the correct expertise.

The hope is that these cross products should be in the editors file by the beginning of January and in the public domain by the end of March.

12th November

I have started trying to work with the files. I loaded up the files list in my import file and made the following notes about what happened.

File warnings:

When I load the files I get two orphans at the top. They are
ID = obol:culmination and
ID = interphase_by_interphase_microtubule_organizing_center

Verification manager warnings on load:

culmination during sorocarp development (GO:0031154) generated 2 warnings:
 The term culmination during sorocarp development (GO:0031154) links to the dangling identifier obol:culmination  The cross product definition of culmination during sorocarp development (GO:0031154) refers to a dangling parent /obol:culmination\. derived_into (OBO_REL:derived_into) generated 1 warning:  The term derived_into (OBO_REL:derived_into) links to the secondary identifier OBO_REL:derives_from has_improper_part (OBO_REL:has_improper_part) generated 1 warning:  The term has_improper_part (OBO_REL:has_improper_part) links to the obsolete term improper_part_of (OBO_REL:improper_part_of) improper_part_of (OBO_REL:improper_part_of) generated 1 warning:  The term improper_part_of (OBO_REL:improper_part_of) links to the obsolete term has_improper_part (OBO_REL:has_improper_part) interphase microtubule nucleation by interphase microtubule organizing center (GO:0051415) generated 2 warnings:  The term interphase microtubule nucleation by interphase microtubule organizing center (GO:0051415) links to the dangling identifier interphase_by_interphase_microtubule_organizing_center  The cross product definition of interphase microtubule nucleation by interphase microtubule organizing center (GO:0051415) refers to a dangling parent /interphase_by_interphase_microtubule_organizing_center\.

OBO-Edit issues:

If I do a link search for anything that has is intersection then the last column of the results is very wide and cannot be made smaller.

Link Search usage:
Selecting things in the link search results panel does not result in them being shown in the OTE or in the Graph viewer. The OTE moves to a new place but there is no way of knowing which term I should be looking at.

Font size:
The tab on the text editor has its name text much smaller than the text on all the other component tabs.

OBO-Edit ran out of memory and crashed even with the reasoner off on my mac.
Components: 1 OTE, Graphviz Viewer, Graph viewer, text editor, link search + one results panel. The cause of the crash was the graph viewer trying to display a term.
This also happens if I load the files and have a link search + results, a term search (unused), a graph viewer and a parent editor.

Search doesn't remember config settings over restart

These issues have all been added to the tracker.

Processing XP files to be checked mostly by eye

I have written two scripts to help with checking the XP composition. Currently all we have are term names to go on, and I think that having the defs available alongside term names will save time. The scripts are:


The first changes the GO live file to tab-delimited format:

GO:id \t definition

The second takes that file and the XP file with this format:

id: GO:0000022 ! mitotic spindle elongation
intersection_of: GO:0051231 ! spindle elongation
intersection_of: part_of GO:0007067 ! mitosis 

id: GO:0000070 ! mitotic sister chromatid segregation
intersection_of: GO:0007059 ! chromosome segregation
intersection_of: part_of GO:0007067 ! mitosis

and where a term id is quoted it adds in the def of the term underneath as follows:

id: GO:0000022 ! mitotic spindle elongation
def: "Lengthening of the distance between poles of the mitotic spindle." [GOC:mah] 

intersection_of: GO:0051231 ! spindle elongation
def: "The cell cycle process whereby the distance is lengthened between poles of the spindle." [GOC:ai] 

intersection_of: part_of GO:0007067 ! mitosis
def: "Progression through mitosis, the division of the eukaryotic cell nucleus to produce 
two daughter nuclei that, usually, contain the identical chromosome complement to their mother." [GOC:ma, ISBN:0198547684]

=Processing file

I have checked the copy of my file with defs into scratch/xps and I will delete terms from that file as they are checked and found to be fine. The file is called biological_process_xp_self_with_defs.obo.

13th November

I have read right through the file and picked out the terms that need changes. These terms are now the only ones in the file xps/biological_process_xp_self_with_defs.obo. I have also made notes on the things that I noticed and on the specific changes needed in the file xps/biological_process_xp_self_notes.txt.

Next I will start making the changes that are needed and will report back to Chris the things that I found.