POC Technical Issues Page
This page provides a record of the software needs of the POC. When requesting new software, please provide an example of why the software is needed. Also provide the date that the request was first made. If the problem has been solved (either by creation of new software, or through some other means, please provide information on the solution here.
Algorithm for gathering annotations from parts of leaf to either vascular leaf or non-vascular leaf
Original request: March 1, 2011
Why this is needed:
At the POC_Conf._Call_3-1-11 we agreed that in general, it is better to have the part_of children of leaf only be part of the general term leaf, rather than create new terms for vascular parts of and non-vascular parts of. Terms that only occur in one or the other (like leaf endodermis) will only be the child of the appropriate term.
If someone puts an annotation on leaf epidermis for rice, it will be collected by leaf, but not by vascular leaf, even though it should also be on vascular leaf. We will suggest to users that in cases like this, they annotate to both leaf epidermis and vascular leaf. Also, we will write an algorithm that automatically adds the annotations to vascular leaf, in case the curators miss it. It will search for annotations for parts of leaf, then check the taxon ID, and then add the appropriate annotation to either vascular leaf or non-vascular leaf. This will assure that annotations end up on the correct terms, but reduce term inflation.
It is likely that the same issue will come up for other classes, as we add terms and annotations for more taxa.
Fix AmiGO software so it can display has_part relations
-The problem is not just in AmiGO, the has_part relation causes a circularity or cycle, which violates our Directed Acyclic Graph DAG
-Our collaborators (eg; SGN), who uses a Chado schema, also have to remove them (LC)
Linking images to PO
Original request: March 9, 2011, but this has been discussed on and off since 2010, including at the POC meeting at the NYBG in Nov. 2010.
