So called "relational" qualities will induce a related entity to be part of the logic expression defining a phenotype. For example:
> as.phenotype(...)
Phenotype 'ceratobranchial 5 tooth located in ascending limb of ceratobranchial 5 bone'
Linked to states:
label character.label study.label
1 Present Ceratobranchial 5 tooth relative to tip of ascending limb Mabee et al. (2011)
Entities:
ceratobranchial 5 tooth <http://purl.obolibrary.org/obo/UBERON_2000694>
Qualities:
located in <http://purl.obolibrary.org/obo/PATO_0002261>
Towards:
ascending limb of ceratobranchial 5 bone <http://purl.obolibrary.org/obo/UBERON_2002013>
And of course this is the common representation used for all absence phenotypes:
> as.phenotype(phens$id[1])
Phenotype 'ceratobranchial 5 tooth absent'
Linked to states:
label
1
2 toothless
3 absent
4 absent
5 absent
6 tooth-plate edentulous
7 Absent
8 CB5 without teeth
9
10 absent
11 absent
12 absent or small and delicate
13 (1) absent
14 absent
15 The absence of dentition on the fifth ceratobranchial
16 toothless
17 absent or small and delicate
18 Teeth absent on fifth ceratobranchials
19 tooth-plate edentulous
character.label
1
2 Fifth ceratobranchial
3 Ceratobranchial 5 teeth
4 Absence of toothplate on 5. ceratobranchial
5 Fifth ceratobranchial, teeth
6 Number of complete rows of teeth on tooth-plate of fifth ceratobranchial
7 Ceratobranchial 5 tooth
8 Dentition of Fifth Ceratobranchial
9
10 Fifth ceratobranchial, teeth
11 Teeth on fifth ceratobranchial
12 Size of dentition on fifth upper pharyngeal tooth-plate and plate of fifth ceratobranchial
13 Teeth on fifth ceratobranchial
14 Teeth on fifth ceratobranchial
15 The absence of dentition on the fifth ceratobranchial
16 Fifth ceratobranchial
17 Size of dentition on fifth upper pharyngeal tooth-plate and plate of fifth ceratobranchial
18 Teeth absent on fifth ceratobranchials
19 Number of complete rows of teeth on tooth-plate of fifth ceratobranchial
study.label
1 Santini and Tyler (2003)
2 Tyler et al. (2003)
3 Fink and Fink (1981); Fink and Fink (1996)
4 Knudsen et al. (2007)
5 Santini and Tyler (2003)
6 Sidlauskas and Vari (2008)
7 Mabee et al. (2011)
8 Baldwin and Johnson (1996)
9 Santini and Tyler (2003)
10 Santini and Tyler (2003)
11 Poyato-Ariza (1996)
12 Sidlauskas and Vari (2008)
13 Mirande (2019)
14 Grande and Poyato-Ariza (1999)
15 Vari (1983)
16 Tyler and Santini (2005)
17 Dillman et al. (2016)
18 Wiley and Johnson (2010)
19 Dillman et al. (2016)
Entities:
multicellular organism <http://purl.obolibrary.org/obo/UBERON_0000468>
Qualities:
lacks all parts of type <http://purl.obolibrary.org/obo/PATO_0002000>
Towards:
ceratobranchial 5 tooth <http://purl.obolibrary.org/obo/UBERON_2000694>
The suggestion is that using the more general "Related entities" is more appropriate.
This was brought over from #198. @balhoff @wdahdul @diegosasso @pmabee @uyedaj if you feel one way or another about this please vote up (= in favor or changing to "Related entities") or down (= keep it at "Towards").
hlapp
commented
1 year ago
So called "relational" qualities will induce a related entity to be part of the logic expression defining a phenotype. For example:
And of course this is the common representation used for all absence phenotypes:
The suggestion is that using the more general "Related entities" is more appropriate.
This was brought over from #198. @balhoff @wdahdul @diegosasso @pmabee @uyedaj if you feel one way or another about this please vote up (= in favor or changing to "Related entities") or down (= keep it at "Towards").