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PathVisio / pathvisio

PathVisio - pathway editor, visualization and analysis software
http://www.pathvisio.org
Apache License 2.0
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Order of PMID references in GPML #100

Open AlexanderPico opened 6 years ago

AlexanderPico commented 6 years ago

Context: This group of editors want to assign PMIDs to every interaction and have them consistently numbered via citation references. I described some workarounds in the meantime. Perhaps the gist of their request, i.e. reference ordering based on entry (or position in GPML), could be implemented? Not sure if this would break other things or even just break conventions for alphabetical listsings?

Request from miguel@icb.ufmg.br:

we found that every time PathVisio saves a gpml, the number on arrows change because PMIDs are organized in xml as children of the same parent, we can edit the gmpl, it may be opened in PathVisio for inspection, but one shall not save it anymore. Everytime one saves, the xml 2 gpml conversion scrambles the order. For now we will follow your suggestion and manually append a number on the arrow. In the future, if possible, would be very nice to fix this info on the arrow just because it would be better to have the literature ordered as cited, by number, instead of alfabetically. Today, references are alphabetically ordered, and these number on arrows change at each saving. Of ourse they keep attached to the right PMIDs, but note that no table shows Arrow2pubmed number, we just see them as a tag while clicking on the number. Therefore, sorting of these numbers do not have a great meaning. Now that we decided to write a number, we wanted to order the literature by order of citation, otherwise our text will have funny numbers, like if we were in Results and have had cited them before. Ok, we can survive with this. And last, we would love to get the ordered arrows related to comments, we will order them so people will connect the arrow with the Interaction. Ok, we will have to order them like this a1, a2, a3, a4...a9, b1, b2, b3... jusst because the sorting in this column is by string, you know, 1, 10, 11, 12... then 2,20,21... In the future, if you could place a olumn with a number in Interaction table, we can order them and sybchronize with the numbers on arrows. Actually, if you find the person that designed the xml, if they could be ordered there by inclusion of whatever, these number might be fixed and related to the Interaction number. I think it is a good idea. Meanwhile we are almost there. We have around 20 pathways deepely annotated, with a full description reaction by reaction and are working on the deposit with the plan I exposed.

egonw commented 6 years ago

This is what we have identifiers for, not? Is it not possible to use these?

DeniseSl22 commented 5 years ago

@mkutmon , this is the issue we talked about last week