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.

Treating different relations differently when dealing with annotations

Original request: March 9, 2011, but has been discussed earlier.

Under the current rules, all relations are treated equally, so all annotations get passed up from any child to its parent, regardless of the relation.

This works fine for is_a and part_of, but is problem for other relations.

develops_from: Annotations should not pass through the develops from relation. For example, leaf develops_from leaf meristem. If a gene is expressed in a leaf, this does not mean it is expressed in the leaf meristem that it developed from.

has_part: Annotations should pass through has_part backwards, that is from parent to child (in the opposite direction of the arrow). Furthermore, they should only pass through has_part relations when the instance for which the annotation was created comes from a taxon in which the parent term is part_of the child term.

For example: In anther has_part pollen sac, anther is the child, and pollen sac is the parent. Annotation should never go from anther to pollen sac. Annotations should go from pollen sac to anther, but only if they come from an angiosperms.

In order for this to work, the conditions under which annotations should pass through will have to be specified every time a has_part relation is added to the ontology. That means that any class in the PO that has a has_part tag will have to have additional tags specifying the conditions under which annotation should pass through the has_part relation. We would have to create a custom tag for this, perhaps a custom relation, that is conditional. Something along the lines of: if taxon_id=xxxx then treat parent term as part_of child term.

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.

Need to register Plantsystematics.org in the GO dbxref database so we can create shortcut links to their pages.