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RO is an ontology of relations for use with biological ontologies
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Proposed naming convention: names of inverses should reuse the same noun #255

Open cmungall opened 6 years ago

cmungall commented 6 years ago

Not sure how best to formally describe this grammatically, but the basic idea is that the names of inverses should not use a different noun or noun phrase, as this is confusing and adds to cognitive burden of using ontology

OK:

NOT OK:

This would be coordinated with BFO

LEHunter commented 6 years ago

This seems sensible, but there are historical reasons for keeping some of these (e.g. bearer/inheres). Would it be acceptable to you to at least keep the old names as synonyms? Or, if there is serious pushback (e.g. from BFO, which has its own needs), having your new names as synonyms?

phismith commented 6 years ago

On Fri, Sep 7, 2018 at 2:03 PM Chris Mungall notifications@github.com wrote:

Not sure how best to formally describe this grammatically, but the basic idea is that the names of inverses should not use a different noun or noun phrase, as this is confusing and adds to cognitive burden of using ontology

OK:

  • part-of / has-part
  • bearer-of / has-bearer

NOT OK:

This would be coordinated with BFO

Does this mean that you propose deprecate 'inheres-in'? Also are you proposing to rename 'generically depends on' and call it 'has-carrier' If not how would you formulate the inverse of 'generically depends on'? Another case in the current BFO-ISO proposal is:

Definition: *b environs c =Def. c occurs in *b [211-ISO]

            Domain: *material entity *or *immaterial entity *but

not spatial region

Range: process or process boundary

Example: mouth environs process of mastication, city environs traffic

What would be your proposal for the inverse of 'occurs in' ?

BS

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msinclair2 commented 6 years ago

Ok, I am a neophyte and I realize my inexperience may contribute to me saying something silly, so I apologize in advance, but here is my opinion:

I think that formulaic rules should not be imposed on the naming of relations. For me, having names of inverses that do not involve the same noun or noun-phrase does not make the ontology more confusing or add to the cognitive burden. For me, distinctiveness makes things easier to remember.

I think there should be leeway to choose a name with connotations that are instructive of the entities that they relate. That is why I like 'inheres in'. Inherence connotes a tight, perhaps inseparable, relationship that describes how an SDC cannot exist without an IC in a way that "has bearer" does not.

For this reason I do favor a change from "generically depends on" to "has carrier". "Generically" is just used to separate the relation from "specifically" and its not clear what this generality means. "Has carrier", on the other hand, connotes something more specific, namely that the rider can exist without that particular carrier and can hop from carrier to carrier or have multiple carriers.

Unless there is a need for automated, computer generation of relation names, I wouldn't like to see a hard and fast rule that interferes with the ontologist's freedom to choose a name with the most instructive connotations.

That said, I think it would be possible in most cases to follow the proposed naming scheme, I just think it should be a guideline and not a rule.

bpeters42 commented 6 years ago

I 100% agree with Chris. Especially for relations that are used 'OBO wide', where we have a lot of relations from different domains that need to be clearly distinguishable when viewed side by side. This is already difficult for the relations themselves, having hard-to-identify inverses makes it worse. In addition, using something like 'carrier of' which is overloaded with mosquitoes carrying pathogens, ships carrying cargo etc. So for information at least, I would go with 'information is carried in' vs. 'carries information'.

phismith commented 6 years ago

What would you call the inverse of 'generically depends on'; what would you call the inverse of 'occurs in'? *where mastication is a process that occurs_in mouth

bpeters42 commented 6 years ago

inv of "generically depends on", could be "has generic dependent" (but I hated those relations from the start, and would much rather keep it to information only anyway) inv of 'occurs in' could be 'has occurent', and again it reveals to me that the relations aren't named precise enough. Much better would be "occurs in location" and "is location of occurent"

On Sat, Sep 8, 2018 at 10:07 AM Barry Smith notifications@github.com wrote:

What would you call the inverse of 'generically depends on'; what would you call the inverse of 'occurs in'? *where mastication is a process that occurs_in mouth

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phismith commented 6 years ago

BS Simplified proposal responding to Chris Mungall’s idea for regimentation of inverse relational expressions:

Grandfather in inheres-in/bearer-of

For inverse of ‘A generically depends on B’ we write:

B is generically depended on by A,

With synonym: B is carrier of A

For ‘A specifically depends on B’ we write

B is specifically depended on by A

If we agree on these then they will be used in BFO-ISO.

On Sat, Sep 8, 2018 at 1:42 PM bpeters42 notifications@github.com wrote:

inv of "generically depends on", could be "has generic dependent" (but I hated those relations from the start, and would much rather keep it to information only anyway) inv of 'occurs in' could be 'has occurent', and again it reveals to me that the relations aren't named precise enough. Much better would be "occurs in location" and "is location of occurent"

On Sat, Sep 8, 2018 at 10:07 AM Barry Smith notifications@github.com wrote:

What would you call the inverse of 'generically depends on'; what would you call the inverse of 'occurs in'? *where mastication is a process that occurs_in mouth

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phismith commented 6 years ago

What shall be our solution for 'occurs in'

ExampleS: a process of digestion occurs in the interior of an organism, a process of loading artillery rounds into a tank cannon occurs in the interior of the tank

Someone suggested:

Definition: *b environs c =Def. c occurs in *b [211-ISO]

            Domain: *material entity *or *immaterial entity *but

not spatial region

Range: process or process boundary

Example: mouth environs process of mastication, city environs traffic

On Tue, Sep 11, 2018 at 1:15 PM Barry Smith phismith@buffalo.edu wrote:

BS Simplified proposal responding to Chris Mungall’s idea for regimentation of inverse relational expressions:

Grandfather in inheres-in/bearer-of

For inverse of ‘A generically depends on B’ we write:

B is generically depended on by A,

With synonym: B is carrier of A

For ‘A specifically depends on B’ we write

B is specifically depended on by A

If we agree on these then they will be used in BFO-ISO.

On Sat, Sep 8, 2018 at 1:42 PM bpeters42 notifications@github.com wrote:

inv of "generically depends on", could be "has generic dependent" (but I hated those relations from the start, and would much rather keep it to information only anyway) inv of 'occurs in' could be 'has occurent', and again it reveals to me that the relations aren't named precise enough. Much better would be "occurs in location" and "is location of occurent"

On Sat, Sep 8, 2018 at 10:07 AM Barry Smith notifications@github.com wrote:

What would you call the inverse of 'generically depends on'; what would you call the inverse of 'occurs in'? *where mastication is a process that occurs_in mouth

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/oborel/obo-relations/issues/255#issuecomment-419658191 , or mute the thread < https://github.com/notifications/unsubscribe-auth/ANN9Iqq3_aRMupN2naM6ONy9jSPwhTM6ks5uY_lVgaJpZM4WfPuz

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-- Bjoern Peters Professor La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

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LEHunter commented 6 years ago

“environs” is defined in Websters dictionary as a noun, not a verb, so this is agrammatical as well as unintuitive.

what’s wrong with “location of / has location”? Why not let “location of / has location” range over both continuants and occurrents? It seems to me that general English does not usually mark this distinction. Mouth location of process of mastication, city location of traffic; as well as Mouth location of tongue and city location of highway.

On Sep 11, 2018, at 1:12 PM, Barry Smith notifications@github.com wrote:

What shall be our solution for 'occurs in'

ExampleS: a process of digestion occurs in the interior of an organism, a process of loading artillery rounds into a tank cannon occurs in the interior of the tank

Someone suggested:

Definition: *b environs c =Def. c occurs in *b [211-ISO]

Domain: material entity or immaterial entity but not spatial region

Range: process or process boundary

Example: mouth environs process of mastication, city environs traffic

On Tue, Sep 11, 2018 at 1:15 PM Barry Smith phismith@buffalo.edu wrote:

BS Simplified proposal responding to Chris Mungall’s idea for regimentation of inverse relational expressions:

Grandfather in inheres-in/bearer-of

For inverse of ‘A generically depends on B’ we write:

B is generically depended on by A,

With synonym: B is carrier of A

For ‘A specifically depends on B’ we write

B is specifically depended on by A

If we agree on these then they will be used in BFO-ISO.

On Sat, Sep 8, 2018 at 1:42 PM bpeters42 notifications@github.com wrote:

inv of "generically depends on", could be "has generic dependent" (but I hated those relations from the start, and would much rather keep it to information only anyway) inv of 'occurs in' could be 'has occurent', and again it reveals to me that the relations aren't named precise enough. Much better would be "occurs in location" and "is location of occurent"

On Sat, Sep 8, 2018 at 10:07 AM Barry Smith notifications@github.com wrote:

What would you call the inverse of 'generically depends on'; what would you call the inverse of 'occurs in'? *where mastication is a process that occurs_in mouth

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/oborel/obo-relations/issues/255#issuecomment-419658191 , or mute the thread < https://github.com/notifications/unsubscribe-auth/ANN9Iqq3_aRMupN2naM6ONy9jSPwhTM6ks5uY_lVgaJpZM4WfPuz

.

-- Bjoern Peters Professor La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

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cmungall commented 6 years ago

Since the first RO paper in 2005 located_in has been used to connect two continuants.

Current BFO2 reference: "The located_in relation links independent continuants which are not spatial regions"

(just realized we lack the D/R constraints, will add...)

I am sympathetic to introducing a grouping relation that is C-vs-O neutral, but it may cause too much churn to try and claim the located_in label for this.

In retrospect, it's clear that RO/BFO frequently claim terms that deceptively sound broader than their intended ontological interpretation. I am always "correcting" biologists who say that some gene product is "part of" a pathway/process, or a process is "located in" a cell. Of course, the biologists are actually correct with respect to the natural terminology of their domain, it's just that BFO/RO uses these terms in a more restricted way. I'm not sure what to do about that for existing relations, but we could do a better job of respecting existing terminology moving forward.

phismith commented 6 years ago

On Tue, Sep 11, 2018 at 3:24 PM Larry Hunter notifications@github.com wrote:

“environs” is defined in Websters dictionary as a noun, not a verb, so this is agrammatical as well as unintuitive.

Verb[edit https://en.wiktionary.org/w/index.php?title=environs&action=edit&section=4 ]

environs

  1. Third-person singular simple present indicative form of environ https://en.wiktionary.org/wiki/environ#English

what’s wrong with “location of / has location”? Why not let “location of / has location” range over both continuants and occurrents? It seems to me that general English does not usually mark this distinction. Mouth location of process of mastication, city location of traffic; as well as Mouth location of tongue and city location of highway.

I am quite willing to give up 'environs' if something better is found, particularly if it is related to 'occurs in' But we cannot remove 'occurs 'in' from BFO, unfortunately. (Too many existing users.) BS

On Sep 11, 2018, at 1:12 PM, Barry Smith notifications@github.com wrote:

What shall be our solution for 'occurs in'

ExampleS: a process of digestion occurs in the interior of an organism, a process of loading artillery rounds into a tank cannon occurs in the interior of the tank

Someone suggested:

Definition: *b environs c =Def. c occurs in *b [211-ISO]

Domain: material entity or immaterial entity but not spatial region

Range: process or process boundary

Example: mouth environs process of mastication, city environs traffic

On Tue, Sep 11, 2018 at 1:15 PM Barry Smith phismith@buffalo.edu wrote:

BS Simplified proposal responding to Chris Mungall’s idea for regimentation of inverse relational expressions:

Grandfather in inheres-in/bearer-of

For inverse of ‘A generically depends on B’ we write:

B is generically depended on by A,

With synonym: B is carrier of A

For ‘A specifically depends on B’ we write

B is specifically depended on by A

If we agree on these then they will be used in BFO-ISO.

On Sat, Sep 8, 2018 at 1:42 PM bpeters42 notifications@github.com wrote:

inv of "generically depends on", could be "has generic dependent" (but I hated those relations from the start, and would much rather keep it to information only anyway) inv of 'occurs in' could be 'has occurent', and again it reveals to me that the relations aren't named precise enough. Much better would be "occurs in location" and "is location of occurent"

On Sat, Sep 8, 2018 at 10:07 AM Barry Smith notifications@github.com

wrote:

What would you call the inverse of 'generically depends on'; what would you call the inverse of 'occurs in'? *where mastication is a process that occurs_in mouth

— You are receiving this because you commented. Reply to this email directly, view it on GitHub <

https://github.com/oborel/obo-relations/issues/255#issuecomment-419658191

, or mute the thread <

https://github.com/notifications/unsubscribe-auth/ANN9Iqq3_aRMupN2naM6ONy9jSPwhTM6ks5uY_lVgaJpZM4WfPuz

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-- Bjoern Peters Professor La Jolla Institute for Allergy and Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/oborel/obo-relations/issues/255#issuecomment-419660474>,

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nlharris commented 4 years ago

What is the status of this?

nlharris commented 3 years ago

@sierra-moxon may have insight into this?