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Myomorpha incorrectly synonymised with Sciurognathi #340

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hyanwong opened this Issue Feb 15, 2017 · 8 comments

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hyanwong commented Feb 15, 2017

If you type in "myomorpha" to the search box, it thinks you are looking for squirrels (Sciurognathi), not the same at all

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Metadata | Do not edit below this line
:------------|:----------
Author | Yan Wong
Upvotes | 0
URL | /contact
Target node label |
Synthetic tree id |
Synthetic tree node id |
Source tree id(s) |
Open Tree Taxonomy id |
Supporting reference | https://en.wikipedia.org/wiki/Myomorpha

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mtholder Feb 15, 2017

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yeah. This is not optimal, but when NCBI's classification does not recognize some subgroups (Myomorpha and Sciuromorpha in this case) of a higher taxon (sciurognathi), it lists the subgroups as synonyms. See https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=33553
which is why OTT treats these as synonyms). I'm not sure that we have an easy fix for this.
Ideally the name Myomorpha would be stored with a taxon concept definition, so that searching for it could return a meaningful message. It would probably still dump the user to the same part of the tree (the parent taxon), but it would be less confusing. But we are pretty far from having taxon concepts under our names/IDs in OTT.

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mtholder commented Feb 15, 2017

yeah. This is not optimal, but when NCBI's classification does not recognize some subgroups (Myomorpha and Sciuromorpha in this case) of a higher taxon (sciurognathi), it lists the subgroups as synonyms. See https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=33553
which is why OTT treats these as synonyms). I'm not sure that we have an easy fix for this.
Ideally the name Myomorpha would be stored with a taxon concept definition, so that searching for it could return a meaningful message. It would probably still dump the user to the same part of the tree (the parent taxon), but it would be less confusing. But we are pretty far from having taxon concepts under our names/IDs in OTT.

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hyanwong Feb 15, 2017

Hmm, this is worse in this instance, because (and I quote for wikipedia) "most researchers do not consider Sciurognathi as an equally valid group. In particular, gundis are thought to be more closely related to the hystricognathous rodents than to other sciurognaths. In spite of this, most texts continue to use these two suborders due primarily to a lack of a viable alternative. Alternatively, some texts group rodents into three suborders on the basis of the shape of the infraorbital canal. According to this taxonomy the rodents are divided into the suborders Sciuromorpha, Hystricomorpha, and Myomorpha."

So it may be that NCBI is not using a monophyletic taxon, which will (presumably) vanish if a correct phylogeny is incorporated.

hyanwong commented Feb 15, 2017

Hmm, this is worse in this instance, because (and I quote for wikipedia) "most researchers do not consider Sciurognathi as an equally valid group. In particular, gundis are thought to be more closely related to the hystricognathous rodents than to other sciurognaths. In spite of this, most texts continue to use these two suborders due primarily to a lack of a viable alternative. Alternatively, some texts group rodents into three suborders on the basis of the shape of the infraorbital canal. According to this taxonomy the rodents are divided into the suborders Sciuromorpha, Hystricomorpha, and Myomorpha."

So it may be that NCBI is not using a monophyletic taxon, which will (presumably) vanish if a correct phylogeny is incorporated.

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hyanwong Feb 15, 2017

@mtholder in fact, myomorphs does exist on the OpenTree, it is simply not named. It is at https://tree.opentreeoflife.org/opentree/opentree8.0@mrcaott42ott55949/Dipodidae--Muroidea. What happens in this case?

hyanwong commented Feb 15, 2017

@mtholder in fact, myomorphs does exist on the OpenTree, it is simply not named. It is at https://tree.opentreeoflife.org/opentree/opentree8.0@mrcaott42ott55949/Dipodidae--Muroidea. What happens in this case?

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If we had this taxon, it would get the name. The trouble is that the only thing that we know about the name is that NCBI lists it as a synonym.
We could fix this with a "patch" to the reference taxonomy. @jar398 would probably need to help in authoring what that would look like. Then the names would not be synonymized in future versions of the tree, and this node would get its label.

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mtholder commented Feb 15, 2017

If we had this taxon, it would get the name. The trouble is that the only thing that we know about the name is that NCBI lists it as a synonym.
We could fix this with a "patch" to the reference taxonomy. @jar398 would probably need to help in authoring what that would look like. Then the names would not be synonymized in future versions of the tree, and this node would get its label.

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hyanwong Feb 15, 2017

Well, for this particular case, Myomorpha is named in e.g. Fabre (2012) which is referenced in OpenTree as a study that resolves this node. So can it simply to be added as a clade name to https://tree.opentreeoflife.org/curator/study/view/pg_2688 or one of those other trees? Or do you not take clade names from phylogenetic studies?

hyanwong commented Feb 15, 2017

Well, for this particular case, Myomorpha is named in e.g. Fabre (2012) which is referenced in OpenTree as a study that resolves this node. So can it simply to be added as a clade name to https://tree.opentreeoflife.org/curator/study/view/pg_2688 or one of those other trees? Or do you not take clade names from phylogenetic studies?

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No. Currently the taxonomy creation is quite separate from the phylogenetic study curation. But thanks for pointing out that study. We have one ad hoc tree provided by taxonomic experts as a taxonomic input. That tree that is used a a source of names and structure. So having a study is helpful.

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mtholder commented Feb 15, 2017

No. Currently the taxonomy creation is quite separate from the phylogenetic study curation. But thanks for pointing out that study. We have one ad hoc tree provided by taxonomic experts as a taxonomic input. That tree that is used a a source of names and structure. So having a study is helpful.

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jar398 Mar 23, 2017

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NCBI distinguishes pro parte synonyms from others, so there is the possibility of being smarter. This happens to be the same question as #341, and I've created OpenTreeOfLife/reference-taxonomy#316 to track it.

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jar398 commented Mar 23, 2017

NCBI distinguishes pro parte synonyms from others, so there is the possibility of being smarter. This happens to be the same question as #341, and I've created OpenTreeOfLife/reference-taxonomy#316 to track it.

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hyanwong Sep 10, 2017

@mtholder this seems low down on the radar, but has been picked up again by one of our users. Is there likely to be any resolution for this in the foreseeable future. Or could I author a patch in some way?

hyanwong commented Sep 10, 2017

@mtholder this seems low down on the radar, but has been picked up again by one of our users. Is there likely to be any resolution for this in the foreseeable future. Or could I author a patch in some way?

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