Uberon claims incorrectly that MESH:A14.254.646 and FMA:56665 are the same #1233

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ChristianKleineidam opened this Issue Jul 7, 2016 · 4 comments

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FMA:56665 is defined as "Skeletal ligament that connects a tooth to maxilla or mandibular".

On the other hand MESH:A14.254.646 is defined as "The structures surrounding and supporting the tooth. Periodontium includes the gum ( GINGIVA), the alveolar bone ( ALVEOLAR PROCESS), the DENTAL CEMENTUM, and the PERIODONTAL LIGAMENT"

The gingiva (FMA:59762) is not part of the skeletal ligament. This issue is confusing because the word Periodontium get's both used as synnonym for Peridontal ligament (FMA lists it as synnonym) and as synnonym for the old Tooth Supporting Structures.

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cmungall Jul 7, 2016

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Yes, I'm not sure FMA is terminologically correct here. We have an editor note

id: UBERON:0001758
name: periodontium
property_value: external_ontology_notes "FMA treats periodontium and periodontal ligament as the same" xsd:string {external_ontology="FMA"}

And also:

id: UBERON:0008266
name: periodontal ligament
property_value: external_ontology_notes "FMA treats periodontium and periodontal ligament as the same; it has a separate class desmodentium, which we place here even though it is classified as fetal in FMA" xsd:string {external_ontology="FMA"}

We should go for logical consistency here rather than terminological. I will make the changes

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cmungall commented Jul 7, 2016

Yes, I'm not sure FMA is terminologically correct here. We have an editor note

id: UBERON:0001758
name: periodontium
property_value: external_ontology_notes "FMA treats periodontium and periodontal ligament as the same" xsd:string {external_ontology="FMA"}

And also:

id: UBERON:0008266
name: periodontal ligament
property_value: external_ontology_notes "FMA treats periodontium and periodontal ligament as the same; it has a separate class desmodentium, which we place here even though it is classified as fetal in FMA" xsd:string {external_ontology="FMA"}

We should go for logical consistency here rather than terminological. I will make the changes

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For some history, see #21

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cmungall commented Jul 7, 2016

For some history, see #21

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ChristianKleineidam Jul 7, 2016

I don't think FMA is wrong. It's just using a term that has polysemy different then MeSH does.
The German Wikipedia happens to list periodontium as a synnonym for periodontal ligament as early as 2005 (https://de.wikipedia.org/w/index.php?title=Wurzelhaut&oldid=11148364). Other websites like http://www.zahn-lexikon.com/index.php/w/50-faqs/497-wurzelhaut also suggest that periodontium is a synnonym in some contexts.

It's like FMA usage of words like arm for (upper arm) or leg (for lower leg) whether other people mean something more general with the words doesn't seem to bother FMA.

I don't think FMA is wrong. It's just using a term that has polysemy different then MeSH does.
The German Wikipedia happens to list periodontium as a synnonym for periodontal ligament as early as 2005 (https://de.wikipedia.org/w/index.php?title=Wurzelhaut&oldid=11148364). Other websites like http://www.zahn-lexikon.com/index.php/w/50-faqs/497-wurzelhaut also suggest that periodontium is a synnonym in some contexts.

It's like FMA usage of words like arm for (upper arm) or leg (for lower leg) whether other people mean something more general with the words doesn't seem to bother FMA.

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On 7 Jul 2016, at 9:25, Christian Kleineidam wrote:

It's like FMA usage of words like arm for (upper arm)
or leg (for lower leg) whether other people mean something more
general with the words doesn't seem to bother FMA.

But it bothers a lot of users. I know some anatomists who have been
dumbfounded by the FMA's usage of 'arm' and 'leg'. Also many users don't
read definitions, so it's important to have 'idiot-proof' primary
labels.

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cmungall commented Jul 7, 2016

On 7 Jul 2016, at 9:25, Christian Kleineidam wrote:

It's like FMA usage of words like arm for (upper arm)
or leg (for lower leg) whether other people mean something more
general with the words doesn't seem to bother FMA.

But it bothers a lot of users. I know some anatomists who have been
dumbfounded by the FMA's usage of 'arm' and 'leg'. Also many users don't
read definitions, so it's important to have 'idiot-proof' primary
labels.

@cmungall cmungall closed this in a6bbaf2 Jul 10, 2016

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