Sustainable maintenance of VTO

hlapp commented 6 years ago

In the short term VTO needs updates with new (mainly miniature) taxa.

Consider adopting OTOL taxonomy (OTT) for updates
Many taxa are, however, missing from OTT (e.g. no Catalog of Fishes)
VTO depends on TTO, and TTO update pipeline would be painful

Making updates sustainable suggests using OTT taxonomy synthesis pipeline (and retiring independent maintenance of VTO).

@wdahdul to find point of contact for CoF to get one-off update
@balhoff to contact Mark Holder about taxonomy update (including CoF in Open Tree)

hlapp commented 6 years ago

Research into OpenTree taxonomy:

[ ] @balhoff to estimate (or determine) mismatch rate;
[ ] @wdahdul to look at Guanyang’s work from Phenoscape hackathon regarding matchup of VTO to Open Tree
[ ] @pmabee to contact CalAcad maintainers re: COF status

wdahdul commented 6 years ago

The work done at the Phenoscape hackathon on matchup between Open Tree (OTT) and VTO is here: https://github.com/phenoscape/phylopheno See final_presentation for slides. Brief summary of the comparisons:

Taxa in Open Tree matched to VTO (for Siluriformes - catfishes): 1:1 match: 68.5% No match: 29% 2+ matches: 2.4%

Taxa in VTO matched to Open Tree (for all VTO?): 40% matched using NCBI IDs as common identifier 48% TNRS exact matches 3% synonyms 9% don’t match

wdahdul commented 6 years ago

From Pasan: File containing lists of mismatched taxa between VTO and OTT for taxa in Jackson et al (2018). Summary numbers:

The number of mismatched taxa that are extinct: 72
The number of mismatched taxa that have ‘sp.’ in their name: 362
The remaining number of mismatched taxa: 940

vto_OT _mismatched taxa from Jackson et al. (2018).docx

balhoff commented 6 years ago

Here are some numbers related to available NCBITaxon xrefs in VTO, using variations of this query:

39289 VTO terms with NCBITaxon xref - 2091 with annotations
67787 VTO terms without NCBITaxon xref - 3370 with annotations

This is just kind of an FYI. Mapping through NCBI is the easiest situation.

balhoff commented 6 years ago

Next step:

[ ] @balhoff will generate list of taxa directly annotated to phenotypes out of those that are not matched to Open Tree.
[ ] @pmabee will follow up with plans for Catalog of Fishes

balhoff commented 6 years ago

This file contains 9109 VTO taxa that couldn't be matched to OTT: https://github.com/phenoscape/PhyloPheno/blob/master/unmatched

Of those, only 563 are used in annotations in the Phenoscape KB. Of those, 354 are "sp." publication taxa, leaving 209 that need to be dealt with:

http://purl.obolibrary.org/obo/VTO_9011043  Acanthodii
http://purl.obolibrary.org/obo/VTO_0069804  Acanthopleurus collettei
http://purl.obolibrary.org/obo/VTO_0069803  Acanthopleurus serratus
http://purl.obolibrary.org/obo/VTO_0069805  Acanthopleurus trispinosus
http://purl.obolibrary.org/obo/VTO_9013283  Acanthostomatops vorax
http://purl.obolibrary.org/obo/VTO_9000404  Acanthothoraciformes
http://purl.obolibrary.org/obo/VTO_0066287  Aethalionopsis robustus
http://purl.obolibrary.org/obo/VTO_9020315  Aistopoda
http://purl.obolibrary.org/obo/VTO_9030507  Anaspida
http://purl.obolibrary.org/obo/VTO_9008281  Andreolepis
http://purl.obolibrary.org/obo/VTO_9023510  Anthracosauroidea
http://purl.obolibrary.org/obo/VTO_9021502  Araeoscelidia
http://purl.obolibrary.org/obo/VTO_9013902  Arandaspidida
http://purl.obolibrary.org/obo/VTO_0070000  Archaeotetraodon jamestyleri
http://purl.obolibrary.org/obo/VTO_0069999  Archaeotetraodon winterbottomi
http://purl.obolibrary.org/obo/VTO_9020545  Ariekanerpeton
http://purl.obolibrary.org/obo/VTO_9000330  Arthrodiriformes
http://purl.obolibrary.org/obo/VTO_0080340  Aspidorhynchus? lepturus
http://purl.obolibrary.org/obo/VTO_9002035  Astraspida
http://purl.obolibrary.org/obo/VTO_9022990  Aztecia
http://purl.obolibrary.org/obo/VTO_0069852  Balistomorphus orbiculatus
http://purl.obolibrary.org/obo/VTO_0069853  Balistomorphus ovalis
http://purl.obolibrary.org/obo/VTO_0069851  Balistomorphus spinosus
http://purl.obolibrary.org/obo/VTO_9000961  Batropetes fritschi
http://purl.obolibrary.org/obo/VTO_0080339  Belonostomus meunsteri
http://purl.obolibrary.org/obo/VTO_9027666  Biarmosuchia
http://purl.obolibrary.org/obo/VTO_0069955  Bolcabalistes varii
http://purl.obolibrary.org/obo/VTO_9033155  Brachythoraci
http://purl.obolibrary.org/obo/VTO_9011733  Brindabellaspis
http://purl.obolibrary.org/obo/VTO_9011701  Campbellodus
http://purl.obolibrary.org/obo/VTO_9004239  Cardiocephalus peabodyi
http://purl.obolibrary.org/obo/VTO_9009890  Cardiocephalus sternbergi
http://purl.obolibrary.org/obo/VTO_0069966  Carpathospinosus propheticus
http://purl.obolibrary.org/obo/VTO_9012740  Cephalaspidiformes
http://purl.obolibrary.org/obo/VTO_0066291  Charitopsis spinosus
http://purl.obolibrary.org/obo/VTO_0066305  Charitosomous lineolatus
http://purl.obolibrary.org/obo/VTO_9016998  Cheliderpeton
http://purl.obolibrary.org/obo/VTO_9031593  Choristodera
http://purl.obolibrary.org/obo/VTO_9021097  Cladodoides
http://purl.obolibrary.org/obo/VTO_9023597  Coccocephalus wildi
http://purl.obolibrary.org/obo/VTO_9030869  Coelurus fragilis
http://purl.obolibrary.org/obo/VTO_9024151  Conodonta
http://purl.obolibrary.org/obo/VTO_0070135  Cretatriacanthus guidottii
http://purl.obolibrary.org/obo/VTO_0069807  Cryptobalistes brevis
http://purl.obolibrary.org/obo/VTO_0066281  Dastilbe crandalli
http://purl.obolibrary.org/obo/VTO_0066282  Dastilbe moraesi
http://purl.obolibrary.org/obo/VTO_9010964  Diabolepis
http://purl.obolibrary.org/obo/VTO_9026884  Dicksonosteus
http://purl.obolibrary.org/obo/VTO_9010171  Dicynodontia
http://purl.obolibrary.org/obo/VTO_9021571  Dinosauromorpha
http://purl.obolibrary.org/obo/VTO_9026251  Diplacanthus ellsi
http://purl.obolibrary.org/obo/VTO_9026255  Diplacanthus horridus
http://purl.obolibrary.org/obo/VTO_9022799  Diplodoselache
http://purl.obolibrary.org/obo/VTO_0066356  Diplomystus shengliensis
http://purl.obolibrary.org/obo/VTO_0066353  Diplomystus solignaci
http://purl.obolibrary.org/obo/VTO_9011027  Doliodus
http://purl.obolibrary.org/obo/VTO_0080324  Domeykos profetaesis
http://purl.obolibrary.org/obo/VTO_0066348  Ellimma branneri
http://purl.obolibrary.org/obo/VTO_0066347  Ellimma riacensis
http://purl.obolibrary.org/obo/VTO_9026925  Enchodus gracilis
http://purl.obolibrary.org/obo/VTO_9017436  Eogyrinus
http://purl.obolibrary.org/obo/VTO_0069815  Eolactoria sorbinii
http://purl.obolibrary.org/obo/VTO_0079064  Eolates aquensis
http://purl.obolibrary.org/obo/VTO_0079065  Eolates gracilis
http://purl.obolibrary.org/obo/VTO_0069813  Eoplectus bloti
http://purl.obolibrary.org/obo/VTO_0069958  Eospinus daniltshenkoi
http://purl.obolibrary.org/obo/VTO_0069837  Eotetraodon pygmaeus
http://purl.obolibrary.org/obo/VTO_0079998  Erichalcis arcta
http://purl.obolibrary.org/obo/VTO_9016143  Euantiarcha
http://purl.obolibrary.org/obo/VTO_9022887  Euconodonta
http://purl.obolibrary.org/obo/VTO_9031550  Euphanerops
http://purl.obolibrary.org/obo/VTO_9000751  Eusthenopteron foordi
http://purl.obolibrary.org/obo/VTO_0041706  Euteleostei
http://purl.obolibrary.org/obo/VTO_9026254  Euthacanthus
http://purl.obolibrary.org/obo/VTO_9002040  Galeaspidiformes
http://purl.obolibrary.org/obo/VTO_0065864  Galeocharax goeldii
http://purl.obolibrary.org/obo/VTO_9034557  Genasauria
http://purl.obolibrary.org/obo/VTO_9022994  Gooloogongia
http://purl.obolibrary.org/obo/VTO_9018461  Gorgonopsia
http://purl.obolibrary.org/obo/VTO_9010794  Griphognathus
http://purl.obolibrary.org/obo/VTO_0066294  Hakeliosomus
http://purl.obolibrary.org/obo/VTO_9030588  Halecomorphi
http://purl.obolibrary.org/obo/VTO_9022800  Harpacanthus
http://purl.obolibrary.org/obo/VTO_0069871  Heptadiodon echinus
http://purl.obolibrary.org/obo/VTO_9023366  Heterostraci
http://purl.obolibrary.org/obo/VTO_0062070  Humboldtichthys kirschbaumi
http://purl.obolibrary.org/obo/VTO_9012951  Hybodus
http://purl.obolibrary.org/obo/VTO_9002426  Hymenochirini
http://purl.obolibrary.org/obo/VTO_0059602  Hypophthalmus longifilis
http://purl.obolibrary.org/obo/VTO_0059311  Hypsidoris farsonensis
http://purl.obolibrary.org/obo/VTO_0059191  Ichthyodectiformes
http://purl.obolibrary.org/obo/VTO_9014377  Ingenia yanshini
http://purl.obolibrary.org/obo/VTO_9011026  Ischnacanthida
http://purl.obolibrary.org/obo/VTO_0060029  Isorineloricaria spinosissma
http://purl.obolibrary.org/obo/VTO_9012346  Jamoytius
http://purl.obolibrary.org/obo/VTO_0066293  Judeichthys haasi
http://purl.obolibrary.org/obo/VTO_9011017  Kathemacanthus
http://purl.obolibrary.org/obo/VTO_9031588  Kenichthys
http://purl.obolibrary.org/obo/VTO_0066503  Knightia bohaiensis
http://purl.obolibrary.org/obo/VTO_9016180  Kujdanowiaspis
http://purl.obolibrary.org/obo/VTO_9001676  Lagerpetidae
http://purl.obolibrary.org/obo/VTO_0059490  Leiocassis similis
http://purl.obolibrary.org/obo/VTO_9022943  Lepidosauromorpha
http://purl.obolibrary.org/obo/VTO_9033975  Ligulalepis
http://purl.obolibrary.org/obo/VTO_0080320  Luisichthys vinalesensis
http://purl.obolibrary.org/obo/VTO_9004371  Luperosaurus kayi
http://purl.obolibrary.org/obo/VTO_0066736  Lycoptera sinensis?
http://purl.obolibrary.org/obo/VTO_9021312  Lysorophia
http://purl.obolibrary.org/obo/VTO_9011630  Macropetalichthys
http://purl.obolibrary.org/obo/VTO_9022464  Maniraptora
http://purl.obolibrary.org/obo/VTO_9012330  Mayomyzon
http://purl.obolibrary.org/obo/VTO_9022802  Medoevia
http://purl.obolibrary.org/obo/VTO_9033435  Meemania
http://purl.obolibrary.org/obo/VTO_0065636  Megacheirodon unicus
http://purl.obolibrary.org/obo/VTO_9030129  Mesophryne beipiaoensis
http://purl.obolibrary.org/obo/VTO_9004227  Microsauria
http://purl.obolibrary.org/obo/VTO_9017542  Mimia toombsi
http://purl.obolibrary.org/obo/VTO_0070119  Moclaybalistes danekrus
http://purl.obolibrary.org/obo/VTO_9023356  Myllokunmingiida
http://purl.obolibrary.org/obo/VTO_9011437  Myriacanthoidei
http://purl.obolibrary.org/obo/VTO_9028450  Nectridea
http://purl.obolibrary.org/obo/VTO_9014194  Odontaspidida
http://purl.obolibrary.org/obo/VTO_0069843  Oligobalistes robustus
http://purl.obolibrary.org/obo/VTO_0069823  Oligolactoria bubiki
http://purl.obolibrary.org/obo/VTO_0061958  Ompok anostomus
http://purl.obolibrary.org/obo/VTO_0061950  Ompok mysoricus
http://purl.obolibrary.org/obo/VTO_9010496  Onychoselache
http://purl.obolibrary.org/obo/VTO_9016708  Ophididae
http://purl.obolibrary.org/obo/VTO_0066343  Ornategulum sardinoides
http://purl.obolibrary.org/obo/VTO_9022471  Ornithomimosauria
http://purl.obolibrary.org/obo/VTO_9023112  Ornithosuchia
http://purl.obolibrary.org/obo/VTO_0059207  Pachythrissops furcatus
http://purl.obolibrary.org/obo/VTO_0066278  Parachanos aethiopicus
http://purl.obolibrary.org/obo/VTO_0066351  Paraclupea chetungensis
http://purl.obolibrary.org/obo/VTO_9017736  Peltobatrachus
http://purl.obolibrary.org/obo/VTO_9000396  Petalichthyiformes
http://purl.obolibrary.org/obo/VTO_9002090  Petromyzontida
http://purl.obolibrary.org/obo/VTO_9033166  Phenacodus intermedius
http://purl.obolibrary.org/obo/VTO_9012179  Pituriaspis
http://purl.obolibrary.org/obo/VTO_9012172  Placodermi
http://purl.obolibrary.org/obo/VTO_0069841  Plectocretacicus clarae
http://purl.obolibrary.org/obo/VTO_0081693  Pliobatrachus
http://purl.obolibrary.org/obo/VTO_9033737  Porolepiformes
http://purl.obolibrary.org/obo/VTO_9008373  Porolepis
http://purl.obolibrary.org/obo/VTO_9008372  Powichthys
http://purl.obolibrary.org/obo/VTO_0070125  Proaracana dubia
http://purl.obolibrary.org/obo/VTO_0069878  Prodiodon erinaceus
http://purl.obolibrary.org/obo/VTO_0069877  Prodiodon tenuispinus
http://purl.obolibrary.org/obo/VTO_0069982  Prohollardia avita
http://purl.obolibrary.org/obo/VTO_0069809  Protacanthodes nimesensis
http://purl.obolibrary.org/obo/VTO_0069810  Protacanthodes ombonii
http://purl.obolibrary.org/obo/VTO_0070130  Protobalistidae
http://purl.obolibrary.org/obo/VTO_0070132  Protobalistum imperialis
http://purl.obolibrary.org/obo/VTO_0080326  Protoclupea atacamensis
http://purl.obolibrary.org/obo/VTO_0080327  Protoclupea chilensis
http://purl.obolibrary.org/obo/VTO_9006134  Protorosauria
http://purl.obolibrary.org/obo/VTO_0069961  Protriacanthus gortanii
http://purl.obolibrary.org/obo/VTO_9021132  Psarolepis
http://purl.obolibrary.org/obo/VTO_0059530  Pseudobagrus pictus
http://purl.obolibrary.org/obo/VTO_0059525  Pseudobagrus taphraphilus
http://purl.obolibrary.org/obo/VTO_0074932  Pseudolabrus crassilabris
http://purl.obolibrary.org/obo/VTO_9005116  Pseudosuchia
http://purl.obolibrary.org/obo/VTO_0069875  Pshekhadiodon parini
http://purl.obolibrary.org/obo/VTO_9000331  Ptyctodontiformes
http://purl.obolibrary.org/obo/VTO_9001337  Ptyonius marshi
http://purl.obolibrary.org/obo/VTO_9000326  Pucapumpella
http://purl.obolibrary.org/obo/VTO_9029052  Rajoidei
http://purl.obolibrary.org/obo/VTO_0066297  Ramallichthys orientalis
http://purl.obolibrary.org/obo/VTO_9000707  Rhamphodopsis
http://purl.obolibrary.org/obo/VTO_9000402  Rhenaniformes
http://purl.obolibrary.org/obo/VTO_9011335  Rhizodonta
http://purl.obolibrary.org/obo/VTO_9026327  Rhyncholepis
http://purl.obolibrary.org/obo/VTO_9004696  Sauropodiformes
http://purl.obolibrary.org/obo/VTO_9026911  Saurorhamphus freyeri
http://purl.obolibrary.org/obo/VTO_9022795  Screbinodus
http://purl.obolibrary.org/obo/VTO_9030428  Silesauridae
http://purl.obolibrary.org/obo/VTO_9016582  Slaugenhopia
http://purl.obolibrary.org/obo/VTO_0066359  Sorbinichthys elusivo
http://purl.obolibrary.org/obo/VTO_9026879  Speonesydrion
http://purl.obolibrary.org/obo/VTO_9015969  Sphenacodontinae
http://purl.obolibrary.org/obo/VTO_0069964  Spinacanthus cuneiformis
http://purl.obolibrary.org/obo/VTO_9033946  Stegotrachelus
http://purl.obolibrary.org/obo/VTO_9018795  Strepsodus sauroides
http://purl.obolibrary.org/obo/VTO_9008395  Strunius
http://purl.obolibrary.org/obo/VTO_9033408  Styloichthys
http://purl.obolibrary.org/obo/VTO_9022752  Synapsida
http://purl.obolibrary.org/obo/VTO_0061823  Synodontis albolineata
http://purl.obolibrary.org/obo/VTO_0061774  Synodontis notata
http://purl.obolibrary.org/obo/VTO_0066285  Tharrhias araripis
http://purl.obolibrary.org/obo/VTO_0066284  Tharrhias rochae
http://purl.obolibrary.org/obo/VTO_9003361  Thelodonti
http://purl.obolibrary.org/obo/VTO_9010240  Therocephalia
http://purl.obolibrary.org/obo/VTO_9017717  Thoosuchus
http://purl.obolibrary.org/obo/VTO_0059199  Thrissops cephalus
http://purl.obolibrary.org/obo/VTO_0069838  Triodon antiquus
http://purl.obolibrary.org/obo/VTO_9004831  Troodon formosus
http://purl.obolibrary.org/obo/VTO_9010782  Uranolophus
http://purl.obolibrary.org/obo/VTO_9020527  Utegenia
http://purl.obolibrary.org/obo/VTO_0080318  Varasichthyidae
http://purl.obolibrary.org/obo/VTO_0080322  Varasichthys ariasi
http://purl.obolibrary.org/obo/VTO_0080343  Vinctifer comptoni
http://purl.obolibrary.org/obo/VTO_0059189  Watsonulus eugnathoides
http://purl.obolibrary.org/obo/VTO_9013444  Xenopus romeri
http://purl.obolibrary.org/obo/VTO_9007300  Yizhoubatrachus macilentus
http://purl.obolibrary.org/obo/VTO_9008383  Youngolepis
http://purl.obolibrary.org/obo/VTO_9013327  Yunnanolepis
http://purl.obolibrary.org/obo/VTO_0061210  Zaireichthys rhodesiensis
http://purl.obolibrary.org/obo/VTO_0069866  Zignodon fornasieroae
http://purl.obolibrary.org/obo/VTO_0069835  Zignoichthys oblongus

phenoscape / vertebrate-taxonomy-ontology

Sustainable maintenance of VTO #3