search

obi-ontology / obi

The Ontology for Biomedical Investigations
http://obi-ontology.org
Creative Commons Attribution 4.0 International
75 stars 25 forks source link

is_orthogonal_to relation #678

Open obi-bot opened 10 years ago

obi-bot commented 10 years ago

Following OBI call held on February 3rd,2014 and Presentation by Heiner Oberkampf,

the need for a new relation 'is_orthogonal_to' is needed to indicate positional property between dimensions being measured. The use case concerns for instance organ/anatomical structures/tumor reported dimensions, not necessarily the organisational dimensions/axis of the organism itself.

note: relate to spatial regions and 'cartesian coordinate datum' ?

Reported by: proccaserra

Original Ticket: obi/obi-terms/692

obi-bot commented 10 years ago

Discussed on the call what domain and range could be. The immediate use case needs this to be between diameters which are in PATO under quality/morphology/1d-extend/length/diameter. Proposals were: Limit domain and range to '1d-extend' qualities (but not all the ones listed would be valid, and this excludes e.g. orthogonality between a line and a plane). Alternatively use 'quality' as domain and range which is rather broad. None of these capture how this is related to 'spatial region' or 'site'. Very specific would be 'has_orthogonal_diameter' with domain and range diameter. This should not offend anyone, and we can always replace with a more general relation later if that is worked out.

Propose this to list; need to import 'diameter'.

Original comment by: bpeters42

obi-bot commented 10 years ago

Original comment by: bpeters42

obi-bot commented 10 years ago

I had an earlier idea about making coordinate systems be information objects about space. In that case orthogonality can be defined on the side of the information object.

However if the use case is anatomy then consider http://www.obofoundry.org/cgi-bin/detail.cgi?id=spatial

Original comment by: alanruttenberg

obi-bot commented 10 years ago

consider coordination with the BSPO property: orthogonal_to http://purl.obolibrary.org/obo/BSPO_0015005

Original comment by: mellybelly

obi-bot commented 10 years ago

Thank you very much for the hint!

The BSPO ontology seems to be very useful for this use case. Probably one could reuse the orthogonal_to relation. The only limitation I see is that the domain and range are 'anatomical axis' and 'anatomical plane'. Do I miss something or is the orthogonal_to relation always between some axis and some plane?

What I would additionally need is orthogonality between two axis (within some plane). Also I would like to use orthogonal relations between lines/axis which are not necessrayly in parallel to the axis as defined under 'anatomical axis' http://purl.obolibrary.org/obo/BSPO_0000010. For example the axis shown in http://www.recist.com/recist-in-practice/19.html are independent of any predefined body axis, but only determined by the form of the measured lymph node and the anatomical plane. How could I do this with BSPO?

Original comment by: heineroberkampf

obi-bot commented 10 years ago

Hi Heiner, You are correct, orthogonal_to is currently defined between a plane and an axis. I agree it could be broadened to include either line/axes or planes. Alternatively, we could create a new property perpendicular_to that only held between anatomical lines. We have a softer property approximately_perpendicular_to that is used similar to your use case, but it is still referring to axes and not to anatomical lines.

I think my recommendation would be to create a new property, perpendicular_to that held between anatomical lines, what do you think? Also, you can put requests on the BSPO tracker, I will move this discussion over there for our records. Thanks melissa

Original comment by: mellybelly

obi-bot commented 10 years ago

BSPO doesn't have a mailing list, but I started a new thread with the BSPO developers on the OBI mailing list:

https://sourceforge.net/p/obi/mailman/obi-devel/thread/1563D9D5-EBEB-46C4-91D4-A090ED7F6277%40overton.ca/#msg32029732

Then one second after hitting "send" I saw Melissa's reply to this tracker item... :^)

Original comment by: jamesaoverton

obi-bot commented 10 years ago

I have just made a tracker item on BSPO for our records (and to get feedback from other anatomists there): https://sourceforge.net/p/obo/common-anatomy-reference-ontology-caro-requests/11/ I think we need a general perpendicular_to relation in BSPO. Whilst mathematically, orthogonality can apply between lines, the usage of this class/label in BSPO has domain and range restrictions to planes and lines and is used to for error checking on the Cartesian components.

Thanks James, the list serve you can use is the anatomy one (cc'd). We will add that to the OBO metadata file so its more obvious. Cheers, Melissa

On Feb 26, 2014, at 6:53 AM, "James A. Overton" jamesaoverton@users.sf.net<mailto:jamesaoverton@users.sf.net> wrote:

BSPO doesn't have a mailing list, but I started a new thread with the BSPO developers on the OBI mailing list:

https://sourceforge.net/p/obi/mailman/obi-devel/thread/1563D9D5-EBEB-46C4-91D4-A090ED7F6277%40overton.ca/#msg32029732

Then one second after hitting "send" I saw Melissa's reply to this tracker item... :^)

[obi-terms:#692]http://sourceforge.net/p/obi/obi-terms/692/ is_orthogonal_to relation

Status: accepted Created: Tue Feb 04, 2014 07:05 PM UTC by Philippe Rocca-Serra Last Updated: Wed Feb 26, 2014 02:46 PM UTC Owner: bjoernpeters

Following OBI call held on February 3rd,2014 and Presentation by Heiner Oberkampf,

the need for a new relation 'is_orthogonal_to' is needed to indicate positional property between dimensions being measured. The use case concerns for instance organ/anatomical structures/tumor reported dimensions, not necessarily the organisational dimensions/axis of the organism itself.

note: relate to spatial regions and 'cartesian coordinate datum' ?

Sent from sourceforge.nethttp://sourceforge.net because you indicated interest in https://sourceforge.net/p/obi/obi-terms/692/

To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

Dr. Melissa Haendel

Assistant Professor Ontology Development Group, OHSU Library www.ohsu.edu/library/ontologyhttp://www.ohsu.edu/library/ontology Department of Medical Informatics and Epidemiology Oregon Health & Science University haendel@ohsu.edumailto:haendel@ohsu.edu skype: melissa.haendel 503-407-5970

Original comment by: mellybelly

obi-bot commented 10 years ago

p.s. This also begs the question - we've had tracker items on the CARO tracker prior for BSPO (where I put this one), but BSPO is now in google code, should we switch?

On Feb 26, 2014, at 6:58 AM, Melissa Haendel haendel@ohsu.edu<mailto:haendel@ohsu.edu> wrote:

I have just made a tracker item on BSPO for our records (and to get feedback from other anatomists there): https://sourceforge.net/p/obo/common-anatomy-reference-ontology-caro-requests/11/ I think we need a general perpendicular_to relation in BSPO. Whilst mathematically, orthogonality can apply between lines, the usage of this class/label in BSPO has domain and range restrictions to planes and lines and is used to for error checking on the Cartesian components.

Thanks James, the list serve you can use is the anatomy one (cc'd). We will add that to the OBO metadata file so its more obvious. Cheers, Melissa

On Feb 26, 2014, at 6:53 AM, "James A. Overton" jamesaoverton@users.sf.net<mailto:jamesaoverton@users.sf.net> wrote:

BSPO doesn't have a mailing list, but I started a new thread with the BSPO developers on the OBI mailing list:

https://sourceforge.net/p/obi/mailman/obi-devel/thread/1563D9D5-EBEB-46C4-91D4-A090ED7F6277%40overton.ca/#msg32029732

Then one second after hitting "send" I saw Melissa's reply to this tracker item... :^)

[obi-terms:#692]http://sourceforge.net/p/obi/obi-terms/692/ is_orthogonal_to relation

Status: accepted Created: Tue Feb 04, 2014 07:05 PM UTC by Philippe Rocca-Serra Last Updated: Wed Feb 26, 2014 02:46 PM UTC Owner: bjoernpeters

Following OBI call held on February 3rd,2014 and Presentation by Heiner Oberkampf,

the need for a new relation 'is_orthogonal_to' is needed to indicate positional property between dimensions being measured. The use case concerns for instance organ/anatomical structures/tumor reported dimensions, not necessarily the organisational dimensions/axis of the organism itself.

note: relate to spatial regions and 'cartesian coordinate datum' ?

Sent from sourceforge.nethttp://sourceforge.net/ because you indicated interest in https://sourceforge.net/p/obi/obi-terms/692/

To unsubscribe from further messages, please visit https://sourceforge.net/auth/subscriptions/

Dr. Melissa Haendel

Assistant Professor Ontology Development Group, OHSU Library www.ohsu.edu/library/ontologyhttp://www.ohsu.edu/library/ontology Department of Medical Informatics and Epidemiology Oregon Health & Science University haendel@ohsu.edumailto:haendel@ohsu.edu skype: melissa.haendel 503-407-5970

Flow-based real-time traffic analytics software. Cisco certified tool. Monitor traffic, SLAs, QoS, Medianet, WAAS etc. with NetFlow Analyzer Customize your own dashboards, set traffic alerts and generate reports. Network behavioral analysis & security monitoring. All-in-one tool. http://pubads.g.doubleclick.net/gampad/clk?id=126839071&iu=/4140/ostg.clktrk_______________________________________________ Obo-anatomy mailing list Obo-anatomy@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/obo-anatomy

Dr. Melissa Haendel

Assistant Professor Ontology Development Group, OHSU Library www.ohsu.edu/library/ontologyhttp://www.ohsu.edu/library/ontology Department of Medical Informatics and Epidemiology Oregon Health & Science University haendel@ohsu.edumailto:haendel@ohsu.edu skype: melissa.haendel 503-407-5970

Original comment by: mellybelly