I have imported the planarian anatomy ontology into PLANP.

When I do a DLQuery for finding all anatomical terms that are part of the visual system I get this:
Query: 'part of' some 'visual system
Results:
'commissural neuron'
'optic chiasma'
'optic cup'
'photoreceptor neuron'
'pigment cup cell'
'trail cell'
eye
owl:Nothing

This looks good.

Using a pattern I generated new terms for each term in PLANA:
text: "'has_part' some ('quality' and ('inheres_in' some %s) and ('qualifier' some 'abnormal'))"

When I query for: ('has part' some ('inheres in' some 'visual system'))
I get nothing.

I would like to find:
'abnormal optic cup', ‘abnormal eye’, etc. but I do not. I only get back 'abnormal visual system'.

When I query for: ('part of' some ('inheres in' some 'visual system'))
I get nothing

How do I need to change my anatomy ontology to get this back? Should I be using ‘has part’ instead of ‘part of’ relationships? Or what am I doing wrong.

Here is what I am thinking about for ventralized/dorsalized/anterioralized/posterioralized animals. Does this look right to everyone?

• abnormal dorsal surface
  • ventralized (PATO_0030003) dorsal surface is ventralized
• abnormal ventral surface
  • dorsalized (PATO_0030001) ventral surface is dorsalized
• abnormal posterior region (or is surface better ??)
  • anterioralized (PATO_0030000) posterior region is anterioralized?
• abnormal anterior region (or is surface better ??)
  • posterioralized (PATO_0030002) anterior region is posterioralized?

The OBO Foundry has recently created a topics page at https://github.com/topics/obofoundry. It would be great if you could add the obofoundry topic to your repository, since it's currently listed as active in the OBO Foundry. If you're not sure how to do that, follow the instructions here. The main issue for this task is at OBOFoundry/OBOFoundry.github.io#1538 in case you want some more context or to join the larger discussion.

There are currently a number of empty synonyms in PLANP which come from an old version of PLANA. Would it be possible to make a new PLANA release, then refresh the PLANA import (ideal all imports) in PLANP and then make a new PLANP release? :)

Thank you!

• total loss of anatomical entity due to degeneration
• abnormal motility of whole organism
• decreased motility of whole organism
• presence of edema MP:edema
• inch worm like movement
• head/tail pinching. hourglass-shaped head/tail? does this work?
• pinching along lateral epithelium
• epithelial ruffles
• bullet hole =? loss of pharynx
• patchy pigmentation. similar pattern to increased/decreased pigmentation? NTR?
• increased fission rate
• scrunched animal?
• animal with extremely visible central nervous system
• animal and tissue lysis

To ensure interoperability between different ontologies, terms in external ontologies such as GO should not be re-defined. For example:

<owl:Class rdf:about="http://purl.obolibrary.org/obo/GO_0007006">
        <owl:equivalentClass>
            <owl:Class>
                <owl:intersectionOf rdf:parseType="Collection">
                    <rdf:Description rdf:about="http://purl.obolibrary.org/obo/GO_0061024"/>
                    <owl:Restriction>
                        <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000066"/>
                        <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PLANA_0007512"/>
                    </owl:Restriction>
                </owl:intersectionOf>
            </owl:Class>
        </owl:equivalentClass>
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0007005"/>
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/GO_0061024"/>
        <rdfs:subClassOf>
            <owl:Restriction>
                <owl:onProperty rdf:resource="http://purl.obolibrary.org/obo/BFO_0000066"/>
                <owl:someValuesFrom rdf:resource="http://purl.obolibrary.org/obo/PLANA_0007512"/>
            </owl:Restriction>
        </rdfs:subClassOf>
        <obo:IAO_0000115 rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a mitochondrial membrane, either of the lipid bilayer surrounding a mitochondrion.</obo:IAO_0000115>
        <oboInOwl:hasExactSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mitochondrial membrane organisation</oboInOwl:hasExactSynonym>
        <oboInOwl:hasOBONamespace rdf:datatype="http://www.w3.org/2001/XMLSchema#string">biological_process</oboInOwl:hasOBONamespace>
        <oboInOwl:hasRelatedSynonym rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mitochondrial membrane organization and biogenesis</oboInOwl:hasRelatedSynonym>
        <oboInOwl:id rdf:datatype="http://www.w3.org/2001/XMLSchema#string">GO:0007006</oboInOwl:id>
        <rdfs:label rdf:datatype="http://www.w3.org/2001/XMLSchema#string">mitochondrial membrane organization</rdfs:label>
    </owl:Class>

You basically re-define a GO term in terms of some PLANA concepts. If you do that, then all ontologies that will use PLANP (such as Upheno, one day!) will inherit that re-definition; with potentially far reaching consequences.