Particularities of the FMA

[cuboideum]

All cranial bones have corresponding subclasses of obo:FMA_83129 ('Bony part of bone organ'), with obo:FMA_52737 ('Temporal bone'), obo:FMA_52739 ('Left temporal bone') and obo:FMA_52738 ('Right temporal bone') being the only exceptions.

I asume this is a bug in the OBO rendering of the FMA. Or is there any reason for treating the temporal bones differently?

This is a complete list of bone organs, for which no subclass of obo:FMA_83129 ('Bony part of bone organ') is defined:

URI oboInOwl.id rdf.schema.label http://purl.obolibrary.org/obo/FMA_33302 FMA:33302 Proximal carpal bone http://purl.obolibrary.org/obo/FMA_33303 FMA:33303 Distal carpal bone http://purl.obolibrary.org/obo/FMA_35495 FMA:35495 First coccygeal vertebra http://purl.obolibrary.org/obo/FMA_35496 FMA:35496 Second coccygeal vertebra http://purl.obolibrary.org/obo/FMA_35497 FMA:35497 Third coccygeal vertebra http://purl.obolibrary.org/obo/FMA_35498 FMA:35498 Fourth coccygeal vertebra http://purl.obolibrary.org/obo/FMA_23951 FMA:23951 Distal phalanx of left thumb http://purl.obolibrary.org/obo/FMA_24459 FMA:24459 Distal phalanx of right thumb http://purl.obolibrary.org/obo/FMA_7595 FMA:7595 Floating rib http://purl.obolibrary.org/obo/FMA_75816 FMA:75816 Proximal phalanx of finger http://purl.obolibrary.org/obo/FMA_75817 FMA:75817 Middle phalanx of finger http://purl.obolibrary.org/obo/FMA_75818 FMA:75818 Distal phalanx of finger http://purl.obolibrary.org/obo/FMA_75828 FMA:75828 Proximal phalanx of toe http://purl.obolibrary.org/obo/FMA_75829 FMA:75829 Middle phalanx of toe http://purl.obolibrary.org/obo/FMA_75830 FMA:75830 Distal phalanx of toe http://purl.obolibrary.org/obo/FMA_52737 FMA:52737 Temporal bone http://purl.obolibrary.org/obo/FMA_24450 FMA:24450 Proximal phalanx of right thumb http://purl.obolibrary.org/obo/FMA_65470 FMA:65470 Proximal phalanx of left thumb http://purl.obolibrary.org/obo/FMA_7592 FMA:7592 True rib http://purl.obolibrary.org/obo/FMA_7594 FMA:7594 False rib http://purl.obolibrary.org/obo/FMA_13077 FMA:13077 First sacral vertebra http://purl.obolibrary.org/obo/FMA_13078 FMA:13078 Second sacral vertebra http://purl.obolibrary.org/obo/FMA_13079 FMA:13079 Third sacral vertebra http://purl.obolibrary.org/obo/FMA_13080 FMA:13080 Fourth sacral vertebra http://purl.obolibrary.org/obo/FMA_13081 FMA:13081 Fifth sacral vertebra http://purl.obolibrary.org/obo/FMA_23889 FMA:23889 Carpal bone http://purl.obolibrary.org/obo/FMA_24491 FMA:24491 Tarsal bone http://purl.obolibrary.org/obo/FMA_75748 FMA:75748 Interparietal bone http://purl.obolibrary.org/obo/FMA_24517 FMA:24517 Cuneiform bone http://purl.obolibrary.org/obo/FMA_52738 FMA:52738 Right temporal bone http://purl.obolibrary.org/obo/FMA_52739 FMA:52739 Left temporal bone http://purl.obolibrary.org/obo/FMA_7593 FMA:7593 Typical rib http://purl.obolibrary.org/obo/FMA_7596 FMA:7596 Atypical rib http://purl.obolibrary.org/obo/FMA_65469 FMA:65469 Lumbar rib http://purl.obolibrary.org/obo/FMA_9913 FMA:9913 Cervical rib http://purl.obolibrary.org/obo/FMA_12526 FMA:12526 Sacral vertebra http://purl.obolibrary.org/obo/FMA_12527 FMA:12527 Coccygeal vertebra http://purl.obolibrary.org/obo/FMA_9139 FMA:9139 Thoracic vertebra http://purl.obolibrary.org/obo/FMA_9915 FMA:9915 Cervical vertebra http://purl.obolibrary.org/obo/FMA_9921 FMA:9921 Lumbar vertebra

EDIT: For the elements referenced by subclasses of class :PrimarySkeletalInventory, this was fixed in the RDFBones patch of the FMA with b471a5d37e09d587e99a2cea68529b7e4831f150.

EDIT: @zarquon42b found out that these omissions seem to be an issue also with the .owl file released by the Structural Informatics Group.

[cuboideum]

The following subclasses of obo:FMA_83129 ('Bony part of bone organ') lack a property statement of type obo:constitutional_part_of, associating them with their corresponding subclasses of FMA:5018 ('bone organ') or obo:FMA_10483 ('Zone of bone organ').

• obo:FMA_42837 ('Bony part of ilium')
  • obo:FMA_46520 ('Bony part of left ilium')
  • obo:FMA_46519 ('Bony part of right ilium')
• obo:FMA_63984 ('Bony part of incus')
  • obo:FMA_63991 ('Bony part of left incus')
  • obo:FMA_63990 ('Bony part of right incus')
• obo:FMA_42851 ('Bony part of ischium')
  • obo:FMA_46530 ('Bony part of left ischium')
  • obo:FMA_46529 ('Bony part of right ischium')
• obo:FMA_63997 ('Bony part of malleus')
• obo:FMA_42844 ('Bony part of pubis')
• obo:FMA_32386 ('Bony part of sacral segment')
  • obo:FMA_32484 ('Bony part of body of sacral segment')
  • obo:FMA_32599 ('Bony part of central part of body of sacral segment')
  • obo:FMA_32600 ('Bony part of posterolateral part of body of sacral segment')
  • obo:FMA_72075 ('Bony part of fifth sacral segment')
  • obo:FMA_31680 ('Bony part of first sacral segment')
  • obo:FMA_72074 ('Bony part of fourth sacral segment')
  • obo:FMA_72072 ('Bony part of second sacral segment')
  • obo:FMA_32602 ('Bony part of superior articular process of first sacral segment')
  • obo:FMA_72073 ('Bony part of third sacral segment')
  • obo:FMA_32492 ('Bony part of vertebral arch of sacral segment')
  • obo:FMA_32494 ('Bony part of lamina of sacral segment')
    • obo:FMA_32502 ('Bony part of lamina of first sacral segment')
    • obo:FMA_32504 ('Bony part of left lamina of first sacral segment')
    • obo:FMA_32503 ('Bony part of right lamina of first sacral segment')
    • obo:FMA_32501 ('Bony part of left lamina of sacral segment')
    • obo:FMA_32500 ('Bony part of right lamina of sacral segment')
  • obo:FMA_32493 ('Bony part of pedicle of sacral segment')
    • obo:FMA_32496 ('Bony part of left pedicle of sacral segment')
    • obo:FMA_32497 ('Bony part of pedicle of first sacral segment')
    • obo:FMA_32495 ('Bony part of right pedicle of sacral segment')
• obo:FMA_232176 ('Bony part of short bone')
• obo:FMA_64004 ('Bony part of stapes')
• obo:FMA_29748 ('Bony part of cervical vertebra')
• obo:FMA_29750 ('Bony part of lumbar vertebra')
• obo:FMA_29749 ('Bony part of thoracic vertebra')

These are obviously mistakes.

EDIT: For the elements referenced by subclasses of class :PrimarySkeletalInventory, this was fixed in the RDFBones patch of the FMA with b471a5d37e09d587e99a2cea68529b7e4831f150.

EDIT: @zarquon42b found out that these omissions seem to be an issue also with the .owl file released by the Structural Informatics Group.

[cuboideum]

Some subclasses of obo:FMA_33535 ('Surface of bone') lack a property statement of obo:bounds, associating them with their corresponding bone organs.

These are obviously mistakes.

EDIT: It is yet unclear if these are errors introduced with the creation of the OBO version or if they are also present in the .owl file released by the Structural Informatics Group.

[cuboideum]

obo:FMA:225573 ('Bony part of twelfth rib) has three restrictions on property obo-fma:constitutional_part_of with the following ranges: obo:FMA_8515 ('Twelfth rib'), obo:FMA_8534 ('Left twelfth rib') and obo:FMA_8533 ('Right twelfth rib'). Obviously, only the first one is correct. The others would be appropriated for the subclasses obo:FMA_225621 ('Bony part of left twelfth rib') and obo:FMA_225619 ('Bony part of right twelfth rib'). These, however, lack the corresponding restrictions.

This is obviously a mistake.

EDIT: Fixed in the RDFBones subset of the FMA with 4720d79418739b3ff024930816889830b90cf30a.

EDIT: It is yet unclear if this is an error introduced with the creation of the OBO version or if they are also present in the .owl file released by the Structural Informatics Group.

[zarquon42b]

Did you find out how to report issues to upstream FMA devs?

[cuboideum]

@zarquon42b With the other bugs, you found out that they are related to the original owl version of the FMA, FMAInOwl, on which the OBO version is based. Consequently, they should be filed with FMAInOwl. However, they do not seem to have a regular bug reporting routine.

For the one concerning the 'Bony part of twelfth rib' class, it is not yet clear whether it lies with FMAInOwl or with the OBO version. Would you like to find out? Or should we file this with the OBOFoundry and ask them to look into it?

[cuboideum]

obo:FMA_225585 ('Bony part of left third rib') has a restriction on the property obo-fma:constitutional_part_of with obo:FMA_8093 ('Left fifth rib') as the defined range. The expected restriction on obo:FMA_8039 ('Left third rib') is also present.

This is obviously a mistake

EDIT: Fixed in the RDFBones subset of the FMA with a1ce41207d3a5426a6c8acab33f0c54f1a1cabde.

EDIT: It is yet unclear if this is an error introduced with the creation of the OBO version or if they are also present in the .owl file released by the Structural Informatics Group.

[cuboideum]

The classes obo:FMA_59415 ('Dental arcade'), obo:FMA_55634 ('Maxillary dental arcade') and obo:FMA_55635 ('Mandibular dental arcade') are all equivalent subclasses of obo:FMA_78590 ('Set of heterogenous clusters'). As maxillary and mandibular dental arcades are types of dental arcades, their classes should be subclasses of obo:FMA_59415 ('Dental arcade').

This is obviously a mistake

@zarquon42b Could you please verify if this is the same in the FmaInOWL version of the FMA?

[zarquon42b]

@cuboideum in upstream FMA:

Dental Arcade is subclass of Heterogeneous anatomical cluster and Maxillary and Mandibular dental arcade inherit this as subclasses of dental arcade

[cuboideum]

@zarquon42b Very well, then we can file an issue with the OBOFoundry.

[cuboideum]

Class obo:FMA_59415 ('Dental arcade') is a subclass of obo:FMA_78590 ('Set of heterogeneous clusters'). In the OWL file released by the Structural Informatics Group at Washington University class fma:59415 ('Dental arcade') is a subclass of fma:64989 ('Heterogeneous anatomical cluster'). In the OBO version this class has another label: obo:FMA_64989 ('Heterogeneous cluster').

This seems to be a bug in the OBO-version of the FMA

[cuboideum]

Classes obo:FMA_78512 ('Set of phalanges of foot') and obo:FMA_71337 ('Set of phalanges of hand') are both subclasses of class obo:FMA_321315 ('Set of phalanges'), which, in turn, is subclass of class obo:FMA_24162 ('Subdivision of skeleton of upper limb'). This makes obo:FMA_78512 ('Set of phalanges of foot') to be a kind (subclass) of obo:FMA_24162 ('Subdivision of skeleton of upper limb').

This is obviously a mistake with the OBO-version of the FMA

@zarquon42b Is it also an issue with the FMAInOwl version?

[zarquon42b]

In FMA: parent of 'Set of phalanges of hand' is 'Subdivision of skeleton of upper limb' (FMA_24162) while 'Set of phalanges of foot' subclass of 'Subdivision of skeleton of lower limb' (FMA_24171), so this issue is obo specific. Both parents are subclasses of 'Subdivision of appendicular skeleton' (FMA_23880)

[cuboideum]

Some classes lack restrictions that should be there in analogy to similar cases (cf. comment to #46).

• _obo:FMA52748 ('Mandible') has a restriction on object properties _obo-fma:systemic_partof and _obo-fma:regional_partof with class _obo:FMA53673 ('Viscerocranium') in the range. Class _obo:FMA9711 ('Maxilla') should have the same restriction.

• _obo:FMA52748 ('Mandible') has a restriction on object property _obo-fma:constitutional_partof with class _obo:FMA54398 ('Lower jaw') in the range. Class _obo:FMA9711 ('Maxilla') should have a similar restriction with _obo:FMA54397 ('Upper jaw') in the range.

• _obo:FMA55640 ('Alveolar arch of maxilla') has a restriction on object property _obo-fma:constitutional_partof with class _obo:FMA54397 ('Upper jaw') in the range. Class _obo:FMA64850 ('Alveolar arch of mandible') should have a similar restriction with _obo:FMA54398 ('Lower jaw') in the range.

• _obo:FMA12516 ('Tooth') has a restriction on object property _obo-fma:regional_partof with class _obo:FMA59415 ('Dental arcade') in the range. Class _obo:FMA57490 ('Tooth socket') should have a similar restriction with _obo:FMA57771 ('Alveolar arch') in the range.

[cuboideum]

The object properties _obo-fma:constitutional_partof and _obo-fma:regional_partof could be made transitive (which is not the case for _obo-fma:systemic_partof).

[15E601]

What is the status of this issue? I recall the email "Upstream FMA suggestions" from 25.11.2020 but not what became of that. Does our subset of the FMA still require tweaking?

[cuboideum]

We still need to to do a bug report to the FMA. So this issue is still active.