search for synonyms #35

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nicolevasilevsky opened this Issue Feb 11, 2015 · 19 comments

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@nicolevasilevsky

Could we add the ability to search for synonyms when searching ontologies in Ontobee?

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cindyJax Feb 11, 2015

I would also find such a feature useful.

I would also find such a feature useful.

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ontoden Feb 11, 2015

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I think Ontobee can already search for synonyms.
You can provide some examples if it is not the case.
Thanks,
Oliver

From: nicolevasilevsky [mailto:notifications@github.com]
Sent: Wednesday, February 11, 2015 4:53 PM
To: ontoden/ontobee
Subject: [ontobee] search for synonyms (#35)

Could we add the ability to search for synonyms when searching ontologies in Ontobee?


Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/35.


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ontoden commented Feb 11, 2015

I think Ontobee can already search for synonyms.
You can provide some examples if it is not the case.
Thanks,
Oliver

From: nicolevasilevsky [mailto:notifications@github.com]
Sent: Wednesday, February 11, 2015 4:53 PM
To: ontoden/ontobee
Subject: [ontobee] search for synonyms (#35)

Could we add the ability to search for synonyms when searching ontologies in Ontobee?


Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/35.


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cindyJax Feb 12, 2015

A search for "vertebral body' does not return 'bony vertebral centrum'

A search for 'von Ebner's gland' does not return 'gustatory gland'

From: ontoden <notifications@github.commailto:notifications@github.com>
Reply-To: ontoden/ontobee <reply@reply.github.commailto:reply@reply.github.com>
Date: Wednesday, February 11, 2015 5:09 PM
To: ontoden/ontobee <ontobee@noreply.github.commailto:ontobee@noreply.github.com>
Cc: Cynthia Smith <cynthia.smith@jax.orgmailto:cynthia.smith@jax.org>
Subject: Re: [ontobee] search for synonyms (#35)

I think Ontobee can already search for synonyms.
You can provide some examples if it is not the case.
Thanks,
Oliver

From: nicolevasilevsky [mailto:notifications@github.com]
Sent: Wednesday, February 11, 2015 4:53 PM
To: ontoden/ontobee
Subject: [ontobee] search for synonyms (#35)

Could we add the ability to search for synonyms when searching ontologies in Ontobee?


Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/35.


Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues


Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/35#issuecomment-73975618.

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A search for "vertebral body' does not return 'bony vertebral centrum'

A search for 'von Ebner's gland' does not return 'gustatory gland'

From: ontoden <notifications@github.commailto:notifications@github.com>
Reply-To: ontoden/ontobee <reply@reply.github.commailto:reply@reply.github.com>
Date: Wednesday, February 11, 2015 5:09 PM
To: ontoden/ontobee <ontobee@noreply.github.commailto:ontobee@noreply.github.com>
Cc: Cynthia Smith <cynthia.smith@jax.orgmailto:cynthia.smith@jax.org>
Subject: Re: [ontobee] search for synonyms (#35)

I think Ontobee can already search for synonyms.
You can provide some examples if it is not the case.
Thanks,
Oliver

From: nicolevasilevsky [mailto:notifications@github.com]
Sent: Wednesday, February 11, 2015 4:53 PM
To: ontoden/ontobee
Subject: [ontobee] search for synonyms (#35)

Could we add the ability to search for synonyms when searching ontologies in Ontobee?


Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/35.


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Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/35#issuecomment-73975618.

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ontoden Feb 12, 2015

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But the term 'bony vertebral centrum' is not a synonym of 'vertebral body':
http://www.ontobee.org/browser/rdf.php?o=VIVO-ISF&iri=http://purl.obolibrary.org/obo/UBERON_0001075

'vertebral body' is indeed a synonym of 'body of vertebra'. The 'body of vertebra' is the label of the term. 'vertebral body' is its synonym. When you search 'vertebral body', Ontobee will return the 'body of vertebra' to you. It indicates that Ontobee can search the synonym.

Oliver


From: cindyJax [notifications@github.com]
Sent: Wednesday, February 11, 2015 7:25 PM
To: ontoden/ontobee
Cc: ontoden
Subject: Re: [ontobee] search for synonyms (#35)

A search for "vertebral body' does not return 'bony vertebral centrum'

A search for 'von Ebner's gland' does not return 'gustatory gland'

From: ontoden <notifications@github.commailto:notifications@github.com>
Reply-To: ontoden/ontobee <reply@reply.github.commailto:reply@reply.github.com>
Date: Wednesday, February 11, 2015 5:09 PM
To: ontoden/ontobee <ontobee@noreply.github.commailto:ontobee@noreply.github.com>
Cc: Cynthia Smith <cynthia.smith@jax.orgmailto:cynthia.smith@jax.org>
Subject: Re: [ontobee] search for synonyms (#35)

I think Ontobee can already search for synonyms.
You can provide some examples if it is not the case.
Thanks,
Oliver

From: nicolevasilevsky [mailto:notifications@github.com]
Sent: Wednesday, February 11, 2015 4:53 PM
To: ontoden/ontobee
Subject: [ontobee] search for synonyms (#35)

Could we add the ability to search for synonyms when searching ontologies in Ontobee?


Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/35.


Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues


Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/35#issuecomment-73975618.

The information in this email, including attachments, may be confidential and is intended solely for the addressee(s). If you believe you received this email by mistake, please notify the sender by return email as soon as possible.


Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/35#issuecomment-73994594.


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ontoden commented Feb 12, 2015

But the term 'bony vertebral centrum' is not a synonym of 'vertebral body':
http://www.ontobee.org/browser/rdf.php?o=VIVO-ISF&iri=http://purl.obolibrary.org/obo/UBERON_0001075

'vertebral body' is indeed a synonym of 'body of vertebra'. The 'body of vertebra' is the label of the term. 'vertebral body' is its synonym. When you search 'vertebral body', Ontobee will return the 'body of vertebra' to you. It indicates that Ontobee can search the synonym.

Oliver


From: cindyJax [notifications@github.com]
Sent: Wednesday, February 11, 2015 7:25 PM
To: ontoden/ontobee
Cc: ontoden
Subject: Re: [ontobee] search for synonyms (#35)

A search for "vertebral body' does not return 'bony vertebral centrum'

A search for 'von Ebner's gland' does not return 'gustatory gland'

From: ontoden <notifications@github.commailto:notifications@github.com>
Reply-To: ontoden/ontobee <reply@reply.github.commailto:reply@reply.github.com>
Date: Wednesday, February 11, 2015 5:09 PM
To: ontoden/ontobee <ontobee@noreply.github.commailto:ontobee@noreply.github.com>
Cc: Cynthia Smith <cynthia.smith@jax.orgmailto:cynthia.smith@jax.org>
Subject: Re: [ontobee] search for synonyms (#35)

I think Ontobee can already search for synonyms.
You can provide some examples if it is not the case.
Thanks,
Oliver

From: nicolevasilevsky [mailto:notifications@github.com]
Sent: Wednesday, February 11, 2015 4:53 PM
To: ontoden/ontobee
Subject: [ontobee] search for synonyms (#35)

Could we add the ability to search for synonyms when searching ontologies in Ontobee?


Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/35.


Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues


Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/35#issuecomment-73975618.

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nicolevasilevsky Feb 13, 2015

Ontobee does not seem to retrieve synonyms from MP. Some examples:

MP Term: increased desmoid tumor incidence
Synonym: musculo-aponeurotic fibromatosis
Synonym: aggressive fibromatosis

MP term: abnormal cochlear hair cell development
Synonym: abnormal auditory hair cell development

image

Ontobee does not seem to retrieve synonyms from MP. Some examples:

MP Term: increased desmoid tumor incidence
Synonym: musculo-aponeurotic fibromatosis
Synonym: aggressive fibromatosis

MP term: abnormal cochlear hair cell development
Synonym: abnormal auditory hair cell development

image

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cmungall Feb 13, 2015

Maybe ontobee doesn't use the oboInOwl vocab?

Maybe ontobee doesn't use the oboInOwl vocab?

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ontoden Feb 14, 2015

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It's possible. Let me check it out.
Oliver


From: Chris Mungall [notifications@github.com]
Sent: Friday, February 13, 2015 6:56 PM
To: ontoden/ontobee
Cc: ontoden
Subject: Re: [ontobee] search for synonyms (#35)

Maybe ontobee doesn't use the oboInOwl vocab?


Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/35#issuecomment-74348354.


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ontoden commented Feb 14, 2015

It's possible. Let me check it out.
Oliver


From: Chris Mungall [notifications@github.com]
Sent: Friday, February 13, 2015 6:56 PM
To: ontoden/ontobee
Cc: ontoden
Subject: Re: [ontobee] search for synonyms (#35)

Maybe ontobee doesn't use the oboInOwl vocab?


Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/35#issuecomment-74348354.


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@cmungall cmungall referenced this issue in obophenotype/uberon Apr 10, 2015

Closed

Term request: Spinal canal at lumbar vertebra #669

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cmungall Apr 28, 2015

Any progress? This should be trivial?

Any progress? This should be trivial?

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ontoden Aug 4, 2015

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The reason why Ontobee could not retrieve synonyms from MP and UBERON is because these two ontologies and several others used:
has_exact_synonym
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
for indicating synonyms.

Ontobee by default used IAO:“alternative term” as synonyms.

After we found the issue, I asked Edison to fix it. Thanks, Edison, for working on this.

This should be fixed in Ontobee by Edison for now. Please check out.

It appears that there are three other types of “synonyms”:
has_related_synonym: http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
has_narrow_synonym: http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
has_broad_synonym: http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym

They appear not “exact”. We don’t know if we want to include these “synonyms” into our synonym searching function. I think we will need to obtain some consensus on this issue first before we implement it.

Oliver

From: nicolevasilevsky [mailto:notifications@github.com]
Sent: Friday, February 13, 2015 2:24 PM
To: ontoden/ontobee
Cc: ontoden
Subject: Re: [ontobee] search for synonyms (#35)

Ontobee does not seem to retrieve synonyms from MP. Some examples:

MP Term: increased desmoid tumor incidence
Synonym: musculo-aponeurotic fibromatosis
Synonym: aggressive fibromatosis

MP term: abnormal cochlear hair cell development
Synonym: abnormal auditory hair cell development

[image]https://cloud.githubusercontent.com/assets/6722114/6193697/b1c17b32-b372-11e4-8d20-6ef5e6867f89.png


Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/35#issuecomment-74310876.


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ontoden commented Aug 4, 2015

The reason why Ontobee could not retrieve synonyms from MP and UBERON is because these two ontologies and several others used:
has_exact_synonym
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
for indicating synonyms.

Ontobee by default used IAO:“alternative term” as synonyms.

After we found the issue, I asked Edison to fix it. Thanks, Edison, for working on this.

This should be fixed in Ontobee by Edison for now. Please check out.

It appears that there are three other types of “synonyms”:
has_related_synonym: http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
has_narrow_synonym: http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
has_broad_synonym: http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym

They appear not “exact”. We don’t know if we want to include these “synonyms” into our synonym searching function. I think we will need to obtain some consensus on this issue first before we implement it.

Oliver

From: nicolevasilevsky [mailto:notifications@github.com]
Sent: Friday, February 13, 2015 2:24 PM
To: ontoden/ontobee
Cc: ontoden
Subject: Re: [ontobee] search for synonyms (#35)

Ontobee does not seem to retrieve synonyms from MP. Some examples:

MP Term: increased desmoid tumor incidence
Synonym: musculo-aponeurotic fibromatosis
Synonym: aggressive fibromatosis

MP term: abnormal cochlear hair cell development
Synonym: abnormal auditory hair cell development

[image]https://cloud.githubusercontent.com/assets/6722114/6193697/b1c17b32-b372-11e4-8d20-6ef5e6867f89.png


Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/35#issuecomment-74310876.


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Hi Chris,
This is the reason.
Edison in my group has now fixed it in Ontobee.
See my previous reply.
Oliver

From: He, Yongqun [mailto:yongqunh@med.umich.edu]
Sent: Friday, February 13, 2015 7:55 PM
To: ontoden/ontobee; ontoden/ontobee
Cc: ontoden
Subject: RE: [ontobee] search for synonyms (#35)

It's possible. Let me check it out.
Oliver


From: Chris Mungall [notifications@github.com]
Sent: Friday, February 13, 2015 6:56 PM
To: ontoden/ontobee
Cc: ontoden
Subject: Re: [ontobee] search for synonyms (#35)

Maybe ontobee doesn't use the oboInOwl vocab?

Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/35#issuecomment-74348354.


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ontoden commented Aug 4, 2015

Hi Chris,
This is the reason.
Edison in my group has now fixed it in Ontobee.
See my previous reply.
Oliver

From: He, Yongqun [mailto:yongqunh@med.umich.edu]
Sent: Friday, February 13, 2015 7:55 PM
To: ontoden/ontobee; ontoden/ontobee
Cc: ontoden
Subject: RE: [ontobee] search for synonyms (#35)

It's possible. Let me check it out.
Oliver


From: Chris Mungall [notifications@github.com]
Sent: Friday, February 13, 2015 6:56 PM
To: ontoden/ontobee
Cc: ontoden
Subject: Re: [ontobee] search for synonyms (#35)

Maybe ontobee doesn't use the oboInOwl vocab?

Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/35#issuecomment-74348354.


Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues


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cmungall Aug 4, 2015

Of course you will want to include the other synonym scopes

cmungall commented Aug 4, 2015

Of course you will want to include the other synonym scopes

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linikujp Aug 4, 2015

I suggest that the broader and narrower synonym terms should be included in
the searching query.

In the result section, those types of synonyms should be shown.

Best,
Asiyah

On Tue, Aug 4, 2015 at 4:21 PM, ontoden notifications@github.com wrote:

The reason why Ontobee could not retrieve synonyms from MP and UBERON is
because these two ontologies and several others used:
has_exact_synonym
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
for indicating synonyms.

Ontobee by default used IAO:“alternative term” as synonyms.

After we found the issue, I asked Edison to fix it. Thanks, Edison, for
working on this.

This should be fixed in Ontobee by Edison for now. Please check out.

It appears that there are three other types of “synonyms”:
has_related_synonym:
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
has_narrow_synonym:
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
has_broad_synonym:
http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym

They appear not “exact”. We don’t know if we want to include these
“synonyms” into our synonym searching function. I think we will need to
obtain some consensus on this issue first before we implement it.

Oliver

From: nicolevasilevsky [mailto:notifications@github.com]
Sent: Friday, February 13, 2015 2:24 PM
To: ontoden/ontobee
Cc: ontoden
Subject: Re: [ontobee] search for synonyms (#35)

Ontobee does not seem to retrieve synonyms from MP. Some examples:

MP Term: increased desmoid tumor incidence
Synonym: musculo-aponeurotic fibromatosis
Synonym: aggressive fibromatosis

MP term: abnormal cochlear hair cell development
Synonym: abnormal auditory hair cell development

[image]<
https://cloud.githubusercontent.com/assets/6722114/6193697/b1c17b32-b372-11e4-8d20-6ef5e6867f89.png>


Reply to this email directly or view it on GitHub<
https://github.com/ontoden/ontobee/issues/35#issuecomment-74310876>.


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be used for urgent or sensitive issues


Reply to this email directly or view it on GitHub
#35 (comment).

linikujp commented Aug 4, 2015

I suggest that the broader and narrower synonym terms should be included in
the searching query.

In the result section, those types of synonyms should be shown.

Best,
Asiyah

On Tue, Aug 4, 2015 at 4:21 PM, ontoden notifications@github.com wrote:

The reason why Ontobee could not retrieve synonyms from MP and UBERON is
because these two ontologies and several others used:
has_exact_synonym
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
for indicating synonyms.

Ontobee by default used IAO:“alternative term” as synonyms.

After we found the issue, I asked Edison to fix it. Thanks, Edison, for
working on this.

This should be fixed in Ontobee by Edison for now. Please check out.

It appears that there are three other types of “synonyms”:
has_related_synonym:
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
has_narrow_synonym:
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
has_broad_synonym:
http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym

They appear not “exact”. We don’t know if we want to include these
“synonyms” into our synonym searching function. I think we will need to
obtain some consensus on this issue first before we implement it.

Oliver

From: nicolevasilevsky [mailto:notifications@github.com]
Sent: Friday, February 13, 2015 2:24 PM
To: ontoden/ontobee
Cc: ontoden
Subject: Re: [ontobee] search for synonyms (#35)

Ontobee does not seem to retrieve synonyms from MP. Some examples:

MP Term: increased desmoid tumor incidence
Synonym: musculo-aponeurotic fibromatosis
Synonym: aggressive fibromatosis

MP term: abnormal cochlear hair cell development
Synonym: abnormal auditory hair cell development

[image]<
https://cloud.githubusercontent.com/assets/6722114/6193697/b1c17b32-b372-11e4-8d20-6ef5e6867f89.png>


Reply to this email directly or view it on GitHub<
https://github.com/ontoden/ontobee/issues/35#issuecomment-74310876>.


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be used for urgent or sensitive issues


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#35 (comment).

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The keyword searching function against has_exact_synonym, has_related_synonym, has_narrow_synonym and has_broad_synonym is now implemented in Ontobee.

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e4ong1031 commented Aug 4, 2015

The keyword searching function against has_exact_synonym, has_related_synonym, has_narrow_synonym and has_broad_synonym is now implemented in Ontobee.

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linikujp Aug 4, 2015

Great! Thanks, Edison!
How about the result page?

On Tue, Aug 4, 2015 at 4:48 PM, e4ong1031 notifications@github.com wrote:

The keyword searching function against has_exact_synonym,
has_related_synonym, has_narrow_synonym and has_broad_synonym is now
implemented in Ontobee.


Reply to this email directly or view it on GitHub
#35 (comment).

linikujp commented Aug 4, 2015

Great! Thanks, Edison!
How about the result page?

On Tue, Aug 4, 2015 at 4:48 PM, e4ong1031 notifications@github.com wrote:

The keyword searching function against has_exact_synonym,
has_related_synonym, has_narrow_synonym and has_broad_synonym is now
implemented in Ontobee.


Reply to this email directly or view it on GitHub
#35 (comment).

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For example,
The term:
http://purl.obolibrary.org/obo/UBERON_0003834
label: thoracic segment blood vessel

has_exact_synonym: thorax blood vessel; blood vessel of thorax
has_related_synonym: upper body blood vessel

Now you can search these synonyms in Ontobee, for example,
http://www.ontobee.org/browser/index.php?keywords=upper+body+blood+vessel&Submit2=Search+terms&o=UBERON

Oliver

From: Asiyah Yu Lin [mailto:notifications@github.com]
Sent: Tuesday, August 04, 2015 4:52 PM
To: ontoden/ontobee
Cc: ontoden
Subject: Re: [ontobee] search for synonyms (#35)

Great! Thanks, Edison!
How about the result page?

On Tue, Aug 4, 2015 at 4:48 PM, e4ong1031 <notifications@github.commailto:notifications@github.com> wrote:

The keyword searching function against has_exact_synonym,
has_related_synonym, has_narrow_synonym and has_broad_synonym is now
implemented in Ontobee.


Reply to this email directly or view it on GitHub
#35 (comment).


Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/35#issuecomment-127758148.


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ontoden commented Aug 4, 2015

For example,
The term:
http://purl.obolibrary.org/obo/UBERON_0003834
label: thoracic segment blood vessel

has_exact_synonym: thorax blood vessel; blood vessel of thorax
has_related_synonym: upper body blood vessel

Now you can search these synonyms in Ontobee, for example,
http://www.ontobee.org/browser/index.php?keywords=upper+body+blood+vessel&Submit2=Search+terms&o=UBERON

Oliver

From: Asiyah Yu Lin [mailto:notifications@github.com]
Sent: Tuesday, August 04, 2015 4:52 PM
To: ontoden/ontobee
Cc: ontoden
Subject: Re: [ontobee] search for synonyms (#35)

Great! Thanks, Edison!
How about the result page?

On Tue, Aug 4, 2015 at 4:48 PM, e4ong1031 <notifications@github.commailto:notifications@github.com> wrote:

The keyword searching function against has_exact_synonym,
has_related_synonym, has_narrow_synonym and has_broad_synonym is now
implemented in Ontobee.


Reply to this email directly or view it on GitHub
#35 (comment).


Reply to this email directly or view it on GitHubhttps://github.com/ontoden/ontobee/issues/35#issuecomment-127758148.


Electronic Mail is not secure, may not be read every day, and should not be used for urgent or sensitive issues

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linikujp Aug 4, 2015

Looks good to me.

Thanks!
Asiyah

On Tue, Aug 4, 2015 at 4:55 PM, ontoden notifications@github.com wrote:

For example,
The term:
http://purl.obolibrary.org/obo/UBERON_0003834
label: thoracic segment blood vessel

has_exact_synonym: thorax blood vessel; blood vessel of thorax
has_related_synonym: upper body blood vessel

Now you can search these synonyms in Ontobee, for example,

http://www.ontobee.org/browser/index.php?keywords=upper+body+blood+vessel&Submit2=Search+terms&o=UBERON

Oliver

From: Asiyah Yu Lin [mailto:notifications@github.com]
Sent: Tuesday, August 04, 2015 4:52 PM
To: ontoden/ontobee
Cc: ontoden
Subject: Re: [ontobee] search for synonyms (#35)

Great! Thanks, Edison!
How about the result page?

On Tue, Aug 4, 2015 at 4:48 PM, e4ong1031 <notifications@github.com
mailto:notifications@github.com> wrote:

The keyword searching function against has_exact_synonym,
has_related_synonym, has_narrow_synonym and has_broad_synonym is now
implemented in Ontobee.


Reply to this email directly or view it on GitHub
#35 (comment).


Reply to this email directly or view it on GitHub<
https://github.com/ontoden/ontobee/issues/35#issuecomment-127758148>.


Electronic Mail is not secure, may not be read every day, and should not
be used for urgent or sensitive issues


Reply to this email directly or view it on GitHub
#35 (comment).

linikujp commented Aug 4, 2015

Looks good to me.

Thanks!
Asiyah

On Tue, Aug 4, 2015 at 4:55 PM, ontoden notifications@github.com wrote:

For example,
The term:
http://purl.obolibrary.org/obo/UBERON_0003834
label: thoracic segment blood vessel

has_exact_synonym: thorax blood vessel; blood vessel of thorax
has_related_synonym: upper body blood vessel

Now you can search these synonyms in Ontobee, for example,

http://www.ontobee.org/browser/index.php?keywords=upper+body+blood+vessel&Submit2=Search+terms&o=UBERON

Oliver

From: Asiyah Yu Lin [mailto:notifications@github.com]
Sent: Tuesday, August 04, 2015 4:52 PM
To: ontoden/ontobee
Cc: ontoden
Subject: Re: [ontobee] search for synonyms (#35)

Great! Thanks, Edison!
How about the result page?

On Tue, Aug 4, 2015 at 4:48 PM, e4ong1031 <notifications@github.com
mailto:notifications@github.com> wrote:

The keyword searching function against has_exact_synonym,
has_related_synonym, has_narrow_synonym and has_broad_synonym is now
implemented in Ontobee.


Reply to this email directly or view it on GitHub
#35 (comment).


Reply to this email directly or view it on GitHub<
https://github.com/ontoden/ontobee/issues/35#issuecomment-127758148>.


Electronic Mail is not secure, may not be read every day, and should not
be used for urgent or sensitive issues


Reply to this email directly or view it on GitHub
#35 (comment).

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cmungall commented Aug 4, 2015

@e4ong1031 you rock!

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cmungall Aug 4, 2015

This has been a major issue for ontobee for a while, it's worth calling out this improvement, e.g. in a news page or tweet

cmungall commented Aug 4, 2015

This has been a major issue for ontobee for a while, it's worth calling out this improvement, e.g. in a news page or tweet

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ontoden Aug 4, 2015

Contributor

Good point. I have added this to the Ontobee news page: http://www.ontobee.org/news.php. Thanks.

Contributor

ontoden commented Aug 4, 2015

Good point. I have added this to the Ontobee news page: http://www.ontobee.org/news.php. Thanks.

@e4ong1031 e4ong1031 closed this Nov 24, 2015

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