obophenotype/biological-spatial-ontology

An ontology for respresenting spatial concepts, anatomical axes, gradients, regions, planes, sides, and surfaces

biological-spatial-ontology's Issues

'opposite to' subClassof 'ipsilateral to'?

Hello,
We at PLANA noticed some strange inferred relationships (example: 'dorsal region' subclassOf 'ventral region'). We tracked it down to 'opposite to' being a subClassOf 'ipsilateral to'.

'opposite to' BSPO:0000113 should not be a child class of 'ipsilateral to' BSPO:0000105 as it is impossible to be both on opposite sides and same sides of something. 'opposite to' BSPO:0000113 will fit better as sibling class to 'part of' BSPO:0000050 (a child class of owl:topObjectProperty)

What is the protocol to make changes to BSPO? Can I edit the owl and make a pull request?

Thanks,
Sofia

midpoints and midlines

It'd be great to have the following terms and definitions:

Midpoint: An anatomical point on the middle part of a structure.

Midline: An anatomical line on the middle of a plane along a structure.

anterior-most

Relabel as 'anterior-most region' to reflect its parent (anatomical region)

Transferred from:
https://sourceforge.net/p/obo/common-anatomy-reference-ontology-caro-requests/10
/

Original issue reported on code.google.com by [email protected] on 13 Jun 2013 at 4:24

"disto-dorsal margin" and "disto-dorsal region"

Can you please add "disto-dorsal margin" and "disto-dorsal region" to BSPO?
Thank you!

orthogonal_to relation

Hi,

There is a previous discussion on the orthogonal_to relation at [2]. 

In BSPO the property orthogonal_to
 - has domain 'anatomical axis' and range 'anatomical plane'.
 - is not symmetric

My considerations:
 a) In my opinion orthogonal_to has to be a symmetric property. This would require that the domain and range are the same: either both undefined or bot the same class. 
 b) In [2] Melissa said, that they need the existing domain and range definitions. So one solution would be to rename the property to has_orthogonal_complement_in_3D and make it a subproperty of orthogonal_to. But even this property should be symmetric in the ideal case.

What do you think?

Best regards,
Heiner

[2] 
http://sourceforge.net/p/obo/common-anatomy-reference-ontology-caro-requests/11/

Original issue reported on code.google.com by [email protected] on 27 Sep 2014 at 1:43

lateral_to

We often use lateral to in arthropod anatomy descriptions (e.g. third cardiac artery is lateral to posterior aorta--'has part' some ('third cardiac artery system' and (lateral_to some ('posterior aorta')))).

Lateral_to is available as an entity from PATO but it would be great to have an object property available from BSPO similar to ventral_to (http://purl.obolibrary.org/obo/BSPO_0000102).

Something like this perhaps:

"x lateral_to y if x is further along the midsagittal plane than y, towards the lateral side."

midsagittal plane is http://purl.obolibrary.org/obo/BSPO_0000009.

Thanks:

István

NCIt Term Suggestions for Cross-Reference

The NCI Cancer Research Data Commons (CRDC) Program (https://datacommons.cancer.gov/) is developing data standards for submitting data to the CRDC ecosystem. As part of this effort, the CRDC Data Standards Service (DSS) Team is identifying industry standards that can be leveraged for this harmonization and standardization effort.

In the process of mapping valid values between various ontologies and NCIt we (the DSS Team) came across terms in the BSPO ontology that either did not have a cross-reference to NCIt terms or that we thought did not cross-reference to the correct NCIt term (please see below):

BSPO Term	BSPO ID	NCIt Term Suggestion for Cross-Reference
proximal to	BSPO:0000100	Proximal (C25236)
in left side of	BSPO:0000120	Left (C25229)
in right side of	BSPO:0000121	Right (C25228)

basal region vs proximal region

Aren't these the same?

http://purl.obolibrary.org/obo/BSPO_0000074

http://purl.obolibrary.org/obo/BSPO_0000077

The same for sides

http://purl.obolibrary.org/obo/BSPO_0000058

http://purl.obolibrary.org/obo/BSPO_0000061

Thanks!

István

new term 'inner surface'

new term needed for 'inner surface'; synonym internal surface

Add identifiers for all relations

Transferred from: 
https://sourceforge.net/p/obo/common-anatomy-reference-ontology-caro-requests/3/

Original issue reported on code.google.com by [email protected] on 13 Jun 2013 at 4:21

Migrate to github

See

https://docs.google.com/document/d/1NfaeHWdZ7BcnaGFfh09X63L4LL7VG_8RNCrLyNdZ8wk/
edit#

still don't know how to preserve users on issues but we have so few doesn't 
really matter

Original issue reported on code.google.com by [email protected] on 13 Mar 2015 at 3:51

central region synonym

Add 'middle region' as a synonym for central region BSPO:0000075

add owl:versionInfo

This should be done by the makefile.

filter untranslatable axioms in obo in release

remove line starting with
owl-axioms: 

Original issue reported on code.google.com by [email protected] on 3 Jul 2013 at 2:23

Two term stanza have wrong date format for the created_date attribute

I am getting an error when loading the obo file for the spatial ontology due to these two term stanzas:
Two terms (stanzas) are using a date-only syntax for the created_date for which the ontology parser are expecting a date/time stamp:

 [Typedef]
 id: BSPO:0000114
 name: lateral to
 def: "X lateral to y if x is further from the midsagittal plane than y." []
 is_transitive: true
 inverse_of: BSPO:0000115 ! medial to
 created_by: Jennifer Girón
 creation_date: 2021-04-21

 [Typedef]
 id: BSPO:0000115
 name: medial to
 name: X medial to y if x is closer to the midsagittal plane than y.
 is_transitive: true
 created_by: Jennifer Girón
 creation_date: 2021-04-21

Is it possible to either remove those two lines or include a full date and time-stamp like in GO.

NR: cranial_to

Required for obophenotype/uberon#697

"cranial" has 2nd class status in bspo at the moment, it's a related syn to 'superior' (in the 'side' branch), which is defined relative to substrate

Definition of anatomical planes

Hi,
I am working on specification of measurements in radiology reports. BSPO many 
usefull classes for anatomical planes and axis which I would like to reuse. 
However I found the following issue:

In human anatomy we have the following three main body planes [1]:
 - sagittal plane: "A sagittal plane, is an anatomical plane which is parallel to the sagittal suture. It divides the body into sinister and dexter (left and right) portions."
 - transverse plane: "A transverse plane is an anatomical plane which devides the body into cranial and caudal (head and tail) portions."
 - coronal plane: "A coronal plane (or frontal plane) is an anatomical plane which divides the body into dorsal and ventral (back and front, or posterior and anterior) portions."

In BSPO we have:
 - 'bspo:sagittal plane': "Anatomical plane that divides a bilateral body into left and right parts, not necessarily of even size."
 - 'bspo:transverse plane': "Anatomical plane that divides body into anterior and posterior parts."
 - 'bspo:horizontal plane': "Anatomical plane that divides bilateral body into dorsal and ventral parts."

Comparison:
 - Defitions of sagittal plane are the same.
 - At Wikipedia [1] I found that (for humans) anterior is the same as ventral and posterior the same as dorsal. I think this is the main issue. Thus (for human anatomy) there is no differnce between 'bspo:transverse plane' and 'bspo:horizontal plane' by their textual definitions in BSPO.
 - A coronal plane is missing in BSPO.

My proposal is to:
 a) change the textal definition of transverse plane to "A transverse plane is an anatomical plane which devides the body into cranial and caudal (head and tail) portions".
 b) add a class 'coronal plane' with definition "A coronal plane (or frontal plane) is an anatomical plane which divides the body into dorsal and ventral parts".

Best regards,
Heiner

[1] http://en.wikipedia.org/wiki/Anatomical_terms_of_location

Original issue reported on code.google.com by [email protected] on 27 Sep 2014 at 1:39

id ranges

@wdahdul @matentzn may I get an idrange to add terms to BSPO?

Align somehow with PATO?

I haven't thought this through, but should this:

biological-spatial-ontology/bspo.obo

Line 1824 in f30f21b

id: opposite_to

be aligned with PATO: https://github.com/pato-ontology/pato/blob/4a927026b5fac9d2809c1eee3be39a9e9284c1dd/pato.obo#L1741

I assume here it is a class, and the other is a property, but just wanted to raise awareness. Feel free to just close if nonsense

Need date in header

Currently, the date tag in the header of the obo-file is not changed but always points to the year 2014. Is it possible to update this date to the current date a change comes out?
My obo parser does not pick up the data-version tag off which I could see if the version has changed.

most part of

Similar to proximalmost part of, could we add the relationships:

lateralmost part of
medialmost part of
anteriormost part of
posteriormost part of

how to cite BSPO?

We would like to cite BSPO in a paper, is there a publication we can use?
It would be very helpful to have citation metadata in this repository, for example as a CITATION.cff file.

'in left side of' and 'in right side of' should not be inverses

Given that Z is an instance of, e.g. 'body', and X and Y are left and right arms:

X 'in left side of' Z
and
Y 'in right side of' Z

Z should not be 'in right side of' X, nor 'in left side of' Y.