ZFIN annotations use BSPO relations as classes

[obophenotype-user]

Originally reported on Google Code with ID 5

Example:

ZP_0007094

Which corresponds to association files with the following 6-tuple:

ZFA:0000360     PATO:0002168    PATO:0000460    ZFA:0001094 BSPO:0000121

i.e.

ZFA:0000360-heart tube          PATO:0002168-displaced to       PATO:0000460-abnormal
  ZFA:0001094-whole organism      BSPO:0000121-in_right_side_of

And generates the nonsensical label:
"abnormal(ly) displaced to heart tube towards whole organism in_right_side_of"

And results in inadvertant punning on the BSPO IRI.

I would recommend that annotators do not attempt to do advanced post-composition, e.g.
using BSPO. It would be better if the ZFIN annotation tools could use the OWLAPI to
detect these issues upstream.

As it is, we need some kind of interim fix for now. This may have to be at the time
of ZP building, requires coordination with Charite

Reported by cmungall on 2013-11-12 20:57:03

[obophenotype-user]

short term fix required: fix monarch import chain to avoid punning

Reported by cmungall on 2013-11-12 20:58:41

[obophenotype-user]

btw, the intended phenotype is obviously:

heart tube displaced to right side of organism

Which is (I presume) homologous to the mammalian phenotype:

[Term]
id: MP:0000644
name: dextrocardia
namespace: MPheno.ontology
alt_id: Fyler:0110
alt_id: Fyler:110
def: "congenital defect in which the heart is located on the right side of the thorax
instead of on the left side (levocardia, the normal position)" [MESH:C14.240.400.280,
MGI:anna]
subset: CvDC_Terms  ! NHLBI Cardiovascular Development Consortium (CvDC) Terms
is_a: MP:0006065  ! abnormal heart position or orientation
intersection_of: PATO:0001793  ! right side of
intersection_of: inheres_in UBERON:0001443 ! chest
intersection_of: towards UBERON:0000948 ! heart

or

[Term]
id: HP:0001651
name: Dextrocardia
namespace: human_phenotype
def: "The heart is located in the right hand sided hemithorax. That is, there is a
left-right reversal (or \"mirror reflection\") of the anatomical location of the heart
in which the heart is locate on the right side instead of the left." [DDD:dbrown, HPO:sdoelken]
synonym: "Thoracic situs inversus" EXACT []
xref: EPCC:02.01.02
xref: ICD-10:Q24.0
xref: MeSH:D003914
xref: UMLS:C0011813
is_a: HP:0004307  ! Abnormal anatomic location of the heart
intersection_of: PATO:0001793  ! right side of
intersection_of: inheres_in FMA:7088 ! Heart
intersection_of: towards FMA:9576 ! Thorax

Contrast this with the ZP owl expression.

3 very different ways of saying pretty much the same thing

Reported by cmungall on 2013-11-12 21:17:03

[drseb]

• [ ] check if this is still happening in ZP
• [ ] discuss with @cindyJax about aligning the logical definitions