evolved-from axioms removed from uberon

[cmungall]

obophenotype/uberon#1270

I just wanted to make sure I had a record of these axioms removed from uberon. Many are present in bgee homology already. However, the directionality is potentially useful (the homology may between two extant classes, but read ontologically, "every limb evolved from a fin" makes sense).

Feel free to pick and choose any of these and close when you like.

I do rather like my narwhal tusk, let's try and preserve that one!

[Term]
id: UBERON:0000024 ! forelimb wing
name: forelimb wing
relationship: evolved_from UBERON:0002102 {subset="musculoskeletal", notes="class will probably be merged into forelimb"} ! forelimb

[Term]
id: UBERON:0001075 ! bony vertebral centrum
name: bony vertebral centrum
relationship: evolved_multiple_times_in NCBITaxon:7742 {source="PMID:11746457", notes="The formation of centra, which is not homologous among vertebrate groups, is acquired independently in some lineages of placoderms, most advanced actinopterygians, and some dipnoans and rhipidistians"} ! Vertebrata

[Term]
id: UBERON:0011907 ! gastrocnemius medialis
name: gastrocnemius medialis
relationship: evolved_from UBERON:0011909 {source="ISBN10:0073040584", subset="musculoskeletal"} ! gastrocnemius internus

[Term]
id: UBERON:0011908 ! gastrocnemius lateralis
name: gastrocnemius lateralis
relationship: evolved_from UBERON:0011910 {source="ISBN10:0073040584", subset="musculoskeletal"} ! gastrocnemius externus

[Term]
id: UBERON:0001687 ! stapes bone
name: stapes bone
relationship: evolved_from UBERON:0011606 {source="VHOG", subset="musculoskeletal"} ! hyomandibular bone

[Term]
id: UBERON:0001688 ! incus bone
name: incus bone
relationship: evolved_from UBERON:0006597 {source="VHOG", subset="musculoskeletal"} ! quadrate bone

[Term]
id: UBERON:0001689 ! malleus bone
name: malleus bone
relationship: evolved_from UBERON:0004744 {source="VHOG", subset="musculoskeletal"} ! articular/anguloarticular

[Term]
id: UBERON:0013477 ! blowhole
name: blowhole
relationship: evolved_from UBERON:0005928 {subset="musculoskeletal"} ! external naris

[Term]
id: UBERON:0002094 ! interventricular septum
name: interventricular septum
relationship: evolved_multiple_times_in NCBITaxon:7742 {source="VHOG:0000386"} ! Vertebrata

[Term]
id: UBERON:0004708 ! paired limb/fin
name: paired limb/fin
relationship: evolved_from UBERON:0002534 {subset="musculoskeletal"} ! paired fin

[Term]
id: UBERON:0002227 ! spiral organ of cochlea
name: spiral organ of cochlea
relationship: evolved_from UBERON:0013731 {subset="musculoskeletal"} ! basilar papilla

[Term]
id: UBERON:0002383 ! supraspinatus muscle
name: supraspinatus muscle
relationship: evolved_from UBERON:0014840 {source="ISBN10:0073040584"} ! supracoracoideus muscle

[Term]
id: UBERON:0001477 ! infraspinatus muscle
name: infraspinatus muscle
relationship: evolved_from UBERON:0014840 {source="ISBN10:0073040584"} ! supracoracoideus muscle

[Term]
id: UBERON:0008976 ! snake venom gland ! snake venom gland
name: snake venom gland
relationship: evolved_from UBERON:0001044 {source="BTO-modified", subset="gland"} ! saliva-secreting gland

[Term]
id: UBERON:0013076 ! snake venom
name: snake venom
relationship: evolved_from UBERON:0001836 {subset="gland", notes="snake venom glands evolved from salibary glands, snake venom is modified saliva"} ! saliva

[Term]
id: UBERON:0015852 ! narwhal tusk ! narwhal tusk
name: narwhal tusk
relationship: evolved_from UBERON:0015850 {source="ISBN10:0073040584"} ! upper left incisor tusk

[ANiknejad]

@fbastian
Frederic, please let me know if there is something to check from my side

[fbastian]

@ANiknejad: could you please make sure that all these "evolved_from" relations are captured in our homology annotations?

@cmungall: didn't you plan to load all the homology assertions into Uberon anyway?

See also obophenotype/uberon#1168 for a reminder

[ANiknejad]

so far in the above list of 'evolved_from', ear related ossicles are captured as is in our homology annotations, I will complete annotations for those missing, thank you

[ANiknejad]

UBERON:0001075 bony vertebral centrum

DONE,
bgee ANN 2017-02-14
PMID:11746457
PMID:25968309
PMID:28144984

[ANiknejad]

reptilian gastrocnemius internus forms gastrocnemius medialis and flexor hallucis longus in mammals (Kardong, p. 388)

http://bio.sunyorange.edu/updated2/comparative_anatomy/anat.html2/M_INTRO.htm

[ANiknejad]

UBERON:0014840|UBERON:0001477|UBERON:0002383 supracoracoideus muscle|infraspinatus muscle|supraspinatus muscle
taxon Amniota
ISBN:978-0253018328
PMID:20807270

DONE

[ANiknejad]

[Term]
id: UBERON:0000024 ! forelimb wing
name: forelimb wing
relationship: evolved_from UBERON:0002102 {subset="musculoskeletal", notes="class will probably be merged into forelimb"} ! forelimb

DONE

UBERON:0000024, UBERON:0002102	forelimb wing, forelimb		HOM:0000007	ISBN:978-0691149776 "Losos JB, The Princeton Guide to Evolution (2014) p.92"	ECO:0000060	positional similarity evidence	CIO:0000004	medium confidence from single evidence	32523	Tetrapoda
UBERON:0000024, UBERON:0002102	forelimb wing, forelimb		HOM:0000007	ISBN:978-0691149776 "Losos JB, The Princeton Guide to Evolution (2014) p.92"	ECO:0000067	developmental similarity evidence	CIO:0000004	medium confidence from single evidence	32523	Tetrapoda
UBERON:0000024, UBERON:0002102	forelimb wing, forelimb		HOM:0000007	ISBN:978-0226313375 "Hall BK, Fins into Limbs: Evolution, Development, and Transformation (2007) p.269"	ECO:0000355	phylogenetic distribution evidence	CIO:0000003	high confidence from single evidence	32524	Amniota
UBERON:0000024, UBERON:0002102	forelimb wing, forelimb		HOM:0000007	ISBN:978-0226313375 "Hall BK, Fins into Limbs: Evolution, Development, and Transformation (2007) p.269"	ECO:0000060	positional similarity evidence	CIO:0000003	high confidence from single evidence	32524	Amniota

[ANiknejad]

[Term]
id: UBERON:0013477 ! blowhole
name: blowhole
relationship: evolved_from UBERON:0005928 {subset="musculoskeletal"} ! external naris

DONE

UBERON:0013477, UBERON:0005928	blowhole, external naris		HOM:0000007	DOI:10.1007/978-3-642-58612-5_1 "Klima M, Development of the Cetacean Nasal Skull. Advances in Anatomy, Embryology and Cell Biology (1999)"	ECO:0000355	phylogenetic distribution evidence	CIO:0000003	high confidence from single evidence	40674	Mammalia
UBERON:0013477, UBERON:0005928	blowhole, external naris		HOM:0000007	DOI:10.1007/978-3-642-58612-5_1 "Klima M, Development of the Cetacean Nasal Skull. Advances in Anatomy, Embryology and Cell Biology (1999)"	ECO:0000067	developmental similarity evidence	CIO:0000003	high confidence from single evidence	40674	Mammalia