forelimb, forelimb wing AND blowhole, ext naris

see #22
BgeeDB · Sep 12, 2017 · 8757028 · 8757028
1 parent 297850f
commit 8757028
Showing 1 changed file with 7 additions and 1 deletion.
diff --git a/edit/bgee_trans_similarity_annotations_edit.tsv b/edit/bgee_trans_similarity_annotations_edit.tsv
@@ -20,7 +20,7 @@
 "OG:0000826"	"foramen caecum"	"issue, in Uberon VHOG:0000826 mapped UBERON:0001761 foramen caecum of thyroid [resolved]"	"UBERON:0006699"	"foramen caecum of tongue"		"HOM:0000007"	"DOI:10.1210/er.2003-0028 ""De Felice M, Di Lauro R, Thyroid development and its disorders: genetics and molecular mechanisms. Endocrine Reviews (2004)"""	"ECO:0000067"	"developmental similarity evidence"	"CIO:0000003"	"High confidence assertion"	40674	"Mammalia"	"By E10, the thyroid primordium appears as a flask-like structure with a narrow neck that rapidly becomes a diverticulum. A small hole at the site of origin in the pharyngeal floor (the foramen cecum) is the remnant of the anlage, connected with the migrating thyroid primordium by a narrow channel (the thyroglossal duct)."	"bgee"	"ANN"	"2015-04-01"	"see https://github.com/obophenotype/uberon/issues/281?source=cc"																																																																					
 "OG:0001566"	"mesovarium"	"ok 1X"	"UBERON:0001342"	"mesovarium"		"HOM:0000007"	"ISBN:978-0072528305 ""Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Chapter 6, Integument, p.560 and Figure 14.23 p.561"""	"ECO:0000355"	"phylogenetic distribution evidence"	"CIO:0000003"	"High confidence assertion"	7742	"Vertebrata"	"The mesovarium is part of female reproductive system in all vertebrates and even present in hagfish. [curator]"	"bgee"	"ANN"	"2013-07-03"																																																																						
 "OG:0001566"	"mesovarium"	"ok 1X"	"UBERON:0001342"	"mesovarium"		"HOM:0000007"	"ISBN:978-0072528305 ""Kardong KV, Vertebrates: Comparative Anatomy, Function, Evolution (2006) Chapter 6, Integument, p.560 and Figure 14.23 p.561"""	"ECO:0000355"	"phylogenetic distribution evidence"	"CIO:0000004"	"Medium confidence assertion"	89593	"Craniata"	"The mesovarium is part of female reproductive system in all vertebrates and even present in hagfish. [curator]"	"bgee"	"ANN"	"2013-07-03"																																																																						
-"//OG:0000671"	"whole organism"	"issue, VHOG:0000671 in Uberon mapped 1x and on UBERON:0000468 multi-cellular organism"	"UBERON:0000467; UBERON:0000468"	"anatomical system, multi-cellular organism"		"HOM:0000007"		"ECO:0000205"	"curator inference"	"CIO:0000003"	"High confidence assertion"	33213	"Bilateria"		"bgee"	"ANN"	"2013-07-03"	"this OG contains the root of the ontologies as well as the term that corresponds to the whole body of the animal; warning: whole organism=FBbt:00007001 (anatomical structure) in Drosophila but some Drosophila data are also reported on FBbt:00000001: organism (which is deeply in the ontology tree...)"																																																																					
+"//OG:0000671"	"whole organism"	"issue, VHOG:0000671 in Uberon mapped 1x and on UBERON:0000468 multi-cellular organism"	"UBERON:0000467, UBERON:0000468"	"anatomical system, multi-cellular organism"		"HOM:0000007"		"ECO:0000205"	"curator inference"	"CIO:0000003"	"High confidence assertion"	33213	"Bilateria"		"bgee"	"ANN"	"2013-07-03"	"this OG contains the root of the ontologies as well as the term that corresponds to the whole body of the animal; warning: whole organism=FBbt:00007001 (anatomical structure) in Drosophila but some Drosophila data are also reported on FBbt:00000001: organism (which is deeply in the ontology tree...)"																																																																					
 "//"	"stages"																																																																																						
 		"has VHOG xref: VHOG:0000745 (zygote) but the VHOG is anatomical, not stage"	"UBERON:0000106"	"zygote stage"		"HOM:0000007"	"ISBN:978-0030259821 ""Ruppert EE, Fox RS, Barnes RD, Invertebrate zoology: a functional evolutionary approach (2003) p.107"""	"ECO:0000034"	"non-traceable author statement"	"CIO:0000003"	"High confidence assertion"	33208	"Metazoa"	"As in all metazoans, eumetazoan development begins with a fertilized egg, or zygote."	"bgee"	"ANN"	"2013-10-04"																																																																						
 			"UBERON:0000066"	"fully formed stage"		"HOM:0000007"	"PMID:23957497 ""Nielsen C, Life cycle evolution: was the eumetazoan ancestor a holopelagic, planktotrophic gastraea? BMC Evol Biol (2013)"""	"ECO:0000034"	"non-traceable author statement"	"CIO:0000003"	"High confidence assertion"	33213	"Bilateria"	"All the available information is strongly in favor of multiple evolution of non-planktotrophic development, and only the terminal addition theory is in accordance with the Darwinian theory by explaining the evolution through continuous series of adaptational changes. This implies that the ancestor of the eumetazoans was a holopelagic, planktotrophic gastraea, and that the adult stages of cnidarians (sessile) and bilaterians (creeping) were later additions to the life cycle. It further implies that the various larval types are of considerable phylogenetic value."	"bgee"	"ANN"	"2013-10-04"	"Bilateria and Cnidaria are sisters, parents = Eumetazoa"																																																																					
@@ -1735,3 +1735,9 @@
 			"UBERON:0001450"	"calcaneus"		"HOM:0000007"	"DOI:10.1002/jez.b.22688 ""Reno PL, Kjosness KM1, Hines JE, The Role of Hox in Pisiform and Calcaneus Growth Plate Formation and the Nature of the Zeugopod/Autopod Boundary. J Exp Zool B Mol Dev Evol (2016)"""	"ECO:0000075"	"gene expression similarity evidence"	"CIO:0000003"	"high confidence from single evidence"	40674	"Mammalia"	"In contrast to the other mesopodials, the mammalian pisiform and calcaneus form true growth plates. We show that these bones, along with other proximal mesopodials, develop within the Hoxa11 and Hoxd11 expression domains."	"bgee"	"ANN"	"2017-06-12"																																																																						
 			"UBERON:0001450"	"calcaneus"		"HOM:0000007"	"DOI:10.1002/jez.b.22688 ""Reno PL, Kjosness KM1, Hines JE, The Role of Hox in Pisiform and Calcaneus Growth Plate Formation and the Nature of the Zeugopod/Autopod Boundary. J Exp Zool B Mol Dev Evol (2016)"""	"ECO:0000067"	"developmental similarity evidence"	"CIO:0000004"	"medium confidence from single evidence"	32523	"Tetrapoda"	"The mammalian calcaneus forms as the combination of two separate condensations which likely shares homology with the fibulare of less derived tetrapods (Cihak, 1972)."	"bgee"	"ANN"	"2017-06-12"																																																																						
 			"UBERON:0001450"	"calcaneus"		"HOM:0000007"	"DOI:10.1002/jez.b.22688 ""Reno PL, Kjosness KM1, Hines JE, The Role of Hox in Pisiform and Calcaneus Growth Plate Formation and the Nature of the Zeugopod/Autopod Boundary. J Exp Zool B Mol Dev Evol (2016)"""	"ECO:0000075"	"gene expression similarity evidence"	"CIO:0000004"	"medium confidence from single evidence"	32523	"Tetrapoda"	"While there is a general correspondence between developmental gene expression and timing of evolutionary origins with the stylopod, zeugopod, and autopod, the correlation is not perfect. The misalignment is highlighted by the growth potential of the pisiform and calcaneus and their residency within particular Hox expression domains supporting a zeugopodial identity (Fig. 8). Such a view better aligns the developmental identity determined in living tetrapods with the evolutionary origin of the proximal mesopodials in sarcopterygians (Fig. 1) prior to the establishment of distal mesopodials and digits."	"bgee"	"ANN"	"2017-06-12"																																																																						
+			"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"	"the forelimb of humans, horses, bats, birds, lizards, and frogs are all homologous to each other as vertebrate forelimbs despite enormous dissimilarities in overall form; the homologies reveal themselves in the major bones present and the patterns by which the bones connect to each other and to the rest of the body; specific homologies of the limb bones and their developmental genetic origins are evident across all four-limbed vertebrates and even among bony fishes. Note that although the forelimbs of bats and birds are homologous as vertebrate forelimbs, they are not homologous as wings. The most recent common ancestor of birds and bats had forelimbs that did not form wings, and the structural modifications that make a bird's forelimb a wing are very different from those that make the bat's forelimb a wing. Bird wings and bat wings thus pass similarity testing as vertebrate forelimbs, but they fail similarity testing as wings."	"bgee"	"ANN"	"2017-09-12"	"see issue https://github.com/BgeeDB/anatomical-similarity-annotations/issues/22"																																																																					
+			"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"	"the forelimb of humans, horses, bats, birds, lizards, and frogs are all homologous to each other as vertebrate forelimbs despite enormous dissimilarities in overall form; the homologies reveal themselves in the major bones present and the patterns by which the bones connect to each other and to the rest of the body; specific homologies of the limb bones and their developmental genetic origins are evident across all four-limbed vertebrates and even among bony fishes. Note that although the forelimbs of bats and birds are homologous as vertebrate forelimbs, they are not homologous as wings. The most recent common ancestor of birds and bats had forelimbs that did not form wings, and the structural modifications that make a bird's forelimb a wing are very different from those that make the bat's forelimb a wing. Bird wings and bat wings thus pass similarity testing as vertebrate forelimbs, but they fail similarity testing as wings."	"bgee"	"ANN"	"2017-09-12"	"see issue https://github.com/BgeeDB/anatomical-similarity-annotations/issues/22"																																																																					
+			"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"	"Because flapping flight originated in both Reptilia (pterosaurs, birds) and Synapsida (bats), the most recent common ancestor of these groups lies at the root of the clade Amniota (e.g., Gauthier et al. 1988b). Following Sumida (1997), we use closely related fossil taxa to reconstruct the forelimb skeleton and pectoral girdle in the hypothetical ancestral amniote. This allow us to characterize wing osteology in each group relative to a common reference point in their evolutionary history."	"bgee"	"ANN"	"2017-09-12"	"see issue https://github.com/BgeeDB/anatomical-similarity-annotations/issues/22 and http://phenoscape.org/wiki/Reasoning_over_homology_statements"																																																																					
+			"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"	"Because flapping flight originated in both Reptilia (pterosaurs, birds) and Synapsida (bats), the most recent common ancestor of these groups lies at the root of the clade Amniota (e.g., Gauthier et al. 1988b). Following Sumida (1997), we use closely related fossil taxa to reconstruct the forelimb skeleton and pectoral girdle in the hypothetical ancestral amniote. This allow us to characterize wing osteology in each group relative to a common reference point in their evolutionary history."	"bgee"	"ANN"	"2017-09-12"	"see issue https://github.com/BgeeDB/anatomical-similarity-annotations/issues/22 and http://phenoscape.org/wiki/Reasoning_over_homology_statements"																																																																					
+			"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"	"The fact that the cetacean nose moved, in the course of evolution, from the tip of the rostrum up to the vertex of the head, is among the most perfect of adaptations to aquatic life. In this and many other special adaptations of their morphology and physiology, cetaceans surpass most primarily aquatic animals even though they themselves have developed from land mammals that breathe with lungs, and have only secondarily conquered the aquatic environment [...] Conclusive paleontological evidence shows the way in which the nasal openings were moved in the course of phylogeny (see Kellogg 1928; Slijper 1962; Gaskin 1976; Oelschlaeger 1978, 1987, 1990; Moore 1981). That this evolutionary process is repeated in a way during ontogeny became obvious through external observations on embryos and fetuses (Kuekenthal 1893). At the earliest embryonic stages the nasal openings are still situated at the rostral tip like those of land mammals; they are gradually shifted more and more towards the vertex of the head at the older stages."	"bgee"	"ANN"	"2017-09-12"	"see issue https://github.com/BgeeDB/anatomical-similarity-annotations/issues/22"																																																																					
+			"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"	"The fact that the cetacean nose moved, in the course of evolution, from the tip of the rostrum up to the vertex of the head, is among the most perfect of adaptations to aquatic life. In this and many other special adaptations of their morphology and physiology, cetaceans surpass most primarily aquatic animals even though they themselves have developed from land mammals that breathe with lungs, and have only secondarily conquered the aquatic environment [...] Conclusive paleontological evidence shows the way in which the nasal openings were moved in the course of phylogeny (see Kellogg 1928; Slijper 1962; Gaskin 1976; Oelschlaeger 1978, 1987, 1990; Moore 1981). That this evolutionary process is repeated in a way during ontogeny became obvious through external observations on embryos and fetuses (Kuekenthal 1893). At the earliest embryonic stages the nasal openings are still situated at the rostral tip like those of land mammals; they are gradually shifted more and more towards the vertex of the head at the older stages."	"bgee"	"ANN"	"2017-09-12"	"see issue https://github.com/BgeeDB/anatomical-similarity-annotations/issues/22"