Open cmungall opened 8 years ago
Public-Health-Bioinformatics
commented
8 years ago I'll take a look at this, and in conjunction with (Thomas Baker's) GACS which has interwoven something like 10,000 terms from AGROVOC and 2 other thesauri into a SKOS product being called a Beta 3.1, see http://tester-os-kktest.lib.helsinki.fi/gacsdemo/gacs/en/ and a slideshow called Global Agricultural Concept Scheme. Got this heads-up from Matthew Lange.
Public-Health-Bioinformatics
commented
7 years ago We'll try to set up Agrovoc coverage as a project within the next year.
cmungall
commented
7 years ago I'm converting a lot of my alignment tools to python, let me know if you need help with this
mateolan
commented
7 years ago So happy to hear you are transitioning to python Chris. Also, I have 2 BioSystems Engineering PhD students, both with MS in CS degrees, starting this Fall, let's get them hacking on your tools ASAP!
On Sun, Aug 6, 2017 at 12:06 PM, Chris Mungall notifications@github.com wrote:
I'm converting a lot of my alignment tools to python, let me know if you need help with this
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ernestojimenezruiz
commented
2 years ago Hi all
This issue is old but I see it is still open, so I was wondering if there are any efforts into the alignment between AGROVOC and FoodOn.
Maybe this could be a challenge for future OAEI editions? This year we have a food-related track: https://oaei.ontologymatching.org/2022/food/index.html
Many thanks in advance!
Best Ernesto
cmungall
commented
2 years ago yes I am interested!
Since this issue was created we have https://github.com/mapping-commons/ and sssom
I haven't been followsing Agrovoc/GACS, should we do separate alignments for each?
So happy to hear you are transitioning to python Chris.
Yes, lexmatch is now a command in https://github.com/INCATools/ontology-access-kit/
mateolan
commented
2 years ago Interested. Are you workshopping this at OAEI and ISWC, if so, do you have dates/times we can attend?
On Fri, Aug 12, 2022 at 4:15 PM Chris Mungall @.***> wrote:
yes I am interested!
Since this issue was created we have https://github.com/mapping-commons/ and sssom
I haven't been followsing Agrovoc/GACS, should we do separate alignments for each?
So happy to hear you are transitioning to python Chris.
Yes, lexmatch is now a command in https://github.com/INCATools/ontology-access-kit/
— Reply to this email directly, view it on GitHub https://github.com/FoodOntology/foodon/issues/6#issuecomment-1213582847, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAMZGIYDRFUNYDVQIJUT2YLVY3LH5ANCNFSM4CCZM3XQ . You are receiving this because you commented.Message ID: @.***>
ddooley
commented
2 years ago It has been a longstanding goal to map FoodOn to Agrovoc - we left this open for that reason - but its been a matter of priorities too. We wanted first to map to USDA SR Legacy single ingredient food samples, and that work is mostly complete, with the creation of over 400 new food terms in FoodOn happening soon (ID's have been assigned). Having accomplished that we expect further mappings to be much easier. Our next objective had been EFSA FoodEx2 mapping, and Agrovoc and GS1 mappings were to follow. We have more curation resources to devote to this.
Any way we can plan to work together to get Agrovoc mapped would be welcome. It would be great if a team could isolate the food product/ingredient terms from Agrovoc that should be covered, so we can see how big the challenge is.
About Siren - LanguaL - FoodOn mapping and INRAE's work, it would be neat to revisit any automated recommendation systems that have arisen from that to see how they would perform with a newer version of FoodOn. SIREN is in fact the core of FoodOn's food product hierarchy (any term that has rdfs:comment SIREN properties listed has in fact originated from SIREN.
ernestojimenezruiz
commented
2 years ago Hi Matthew, Chris, Damion and all
Apologies for the delay. Slowly coming back from holidays.
It may be an interesting topic to discuss during the virtual OM workshop: http://om2022.ontologymatching.org/ (we typically have some open discussions).
We could try to set up a new track for OAEI 2023. As we do not have a ground truth we could try to create a "silver" standard by merging the outputs of different systems (the ones participating in previous OAEIs). We did something similar here: Matching disease and phenotype ontologies in the ontology alignment evaluation initiative | Journal of Biomedical Semantics | Full Text (biomedcentral.com) https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0162-9 For that silver standard sssom would be great as we could also keep track of the provenance of the mappings (which system(s) suggested a mapping)
Best Ernesto
El sáb, 13 ago 2022 a las 3:51, Matthew Lange @.***>) escribió:
Interested. Are you workshopping this at OAEI and ISWC, if so, do you have dates/times we can attend?
On Fri, Aug 12, 2022 at 4:15 PM Chris Mungall @.***> wrote:
yes I am interested!
Since this issue was created we have https://github.com/mapping-commons/ and sssom
I haven't been followsing Agrovoc/GACS, should we do separate alignments for each?
So happy to hear you are transitioning to python Chris.
Yes, lexmatch is now a command in https://github.com/INCATools/ontology-access-kit/
— Reply to this email directly, view it on GitHub <https://github.com/FoodOntology/foodon/issues/6#issuecomment-1213582847 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AAMZGIYDRFUNYDVQIJUT2YLVY3LH5ANCNFSM4CCZM3XQ
. You are receiving this because you commented.Message ID: @.***>
— Reply to this email directly, view it on GitHub https://github.com/FoodOntology/foodon/issues/6#issuecomment-1213638435, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADYLZ6QAG75VVFFH2H6ULV3VY4ESJANCNFSM4CCZM3XQ . You are receiving this because you commented.Message ID: @.***>
-- Ernesto Jiménez-Ruiz Lecturer in Artificial Intelligence
Department of Computer Science School of Science & Technology City, University of London https://www.city.ac.uk/people/academics/ernesto-jimenez-ruiz
mateolan
commented
2 years ago This sounds amazing. Count me in for discussion at the 2022 workshop, and put me on whatever committee I need to be on for 2023 in order to make this happen. This is a big problem all over food systems. Development of term-matching pipelines would advance Food Informatics exponentially. I would also be delighted to discuss/workshop the potential for generalizable pipelines with pluggable vocabs--we could host such a thing at one of our supercomputer facilities at ICICLE.ai Looking forward, ~Matthew
On Thu, Sep 22, 2022 at 1:02 AM Ernesto Jimenez Ruiz < @.***> wrote:
Hi Matthew, Chris, Damion and all
Apologies for the delay. Slowly coming back from holidays.
It may be an interesting topic to discuss during the virtual OM workshop: http://om2022.ontologymatching.org/ (we typically have some open discussions).
We could try to set up a new track for OAEI 2023. As we do not have a ground truth we could try to create a "silver" standard by merging the outputs of different systems (the ones participating in previous OAEIs). We did something similar here: Matching disease and phenotype ontologies in the ontology alignment evaluation initiative | Journal of Biomedical Semantics | Full Text (biomedcentral.com) https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0162-9 For that silver standard sssom would be great as we could also keep track of the provenance of the mappings (which system(s) suggested a mapping)
Best Ernesto
El sáb, 13 ago 2022 a las 3:51, Matthew Lange @.***>) escribió:
Interested. Are you workshopping this at OAEI and ISWC, if so, do you have dates/times we can attend?
On Fri, Aug 12, 2022 at 4:15 PM Chris Mungall @.***> wrote:
yes I am interested!
Since this issue was created we have https://github.com/mapping-commons/ and sssom
I haven't been followsing Agrovoc/GACS, should we do separate alignments for each?
So happy to hear you are transitioning to python Chris.
Yes, lexmatch is now a command in https://github.com/INCATools/ontology-access-kit/
— Reply to this email directly, view it on GitHub < https://github.com/FoodOntology/foodon/issues/6#issuecomment-1213582847 , or unsubscribe <
https://github.com/notifications/unsubscribe-auth/AAMZGIYDRFUNYDVQIJUT2YLVY3LH5ANCNFSM4CCZM3XQ
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-- Ernesto Jiménez-Ruiz Lecturer in Artificial Intelligence
Department of Computer Science School of Science & Technology City, University of London https://www.city.ac.uk/people/academics/ernesto-jimenez-ruiz
— Reply to this email directly, view it on GitHub https://github.com/FoodOntology/foodon/issues/6#issuecomment-1254668135, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAMZGI7SB45A2DH33ZQZDVDV7QHADANCNFSM4CCZM3XQ . You are receiving this because you commented.Message ID: @.***>
ernestojimenezruiz
commented
2 years ago (I keep missing these messages as they are archived in the wrong folder...)
Sounds very good! Let's try to have a chat during the OM workshop (the poster session may be a good time or any of the coffee breaks). We will be using Gather.town: http://om2022.ontologymatching.org/#prg
Ernesto
El jue, 22 sept 2022 a las 18:20, Matthew Lange @.***>) escribió:
This sounds amazing. Count me in for discussion at the 2022 workshop, and put me on whatever committee I need to be on for 2023 in order to make this happen. This is a big problem all over food systems. Development of term-matching pipelines would advance Food Informatics exponentially. I would also be delighted to discuss/workshop the potential for generalizable pipelines with pluggable vocabs--we could host such a thing at one of our supercomputer facilities at ICICLE.ai Looking forward, ~Matthew
On Thu, Sep 22, 2022 at 1:02 AM Ernesto Jimenez Ruiz < @.***> wrote:
Hi Matthew, Chris, Damion and all
Apologies for the delay. Slowly coming back from holidays.
It may be an interesting topic to discuss during the virtual OM workshop: http://om2022.ontologymatching.org/ (we typically have some open discussions).
We could try to set up a new track for OAEI 2023. As we do not have a ground truth we could try to create a "silver" standard by merging the outputs of different systems (the ones participating in previous OAEIs). We did something similar here: Matching disease and phenotype ontologies in the ontology alignment evaluation initiative | Journal of Biomedical Semantics | Full Text (biomedcentral.com) <https://jbiomedsem.biomedcentral.com/articles/10.1186/s13326-017-0162-9
For that silver standard sssom would be great as we could also keep track of the provenance of the mappings (which system(s) suggested a mapping)
Best Ernesto
El sáb, 13 ago 2022 a las 3:51, Matthew Lange @.***>) escribió:
Interested. Are you workshopping this at OAEI and ISWC, if so, do you have dates/times we can attend?
On Fri, Aug 12, 2022 at 4:15 PM Chris Mungall @.***> wrote:
yes I am interested!
Since this issue was created we have https://github.com/mapping-commons/ and sssom
I haven't been followsing Agrovoc/GACS, should we do separate alignments for each?
So happy to hear you are transitioning to python Chris.
Yes, lexmatch is now a command in https://github.com/INCATools/ontology-access-kit/
— Reply to this email directly, view it on GitHub < https://github.com/FoodOntology/foodon/issues/6#issuecomment-1213582847 , or unsubscribe <
https://github.com/notifications/unsubscribe-auth/AAMZGIYDRFUNYDVQIJUT2YLVY3LH5ANCNFSM4CCZM3XQ
. You are receiving this because you commented.Message ID: @.***>
— Reply to this email directly, view it on GitHub < https://github.com/FoodOntology/foodon/issues/6#issuecomment-1213638435 , or unsubscribe <
https://github.com/notifications/unsubscribe-auth/ADYLZ6QAG75VVFFH2H6ULV3VY4ESJANCNFSM4CCZM3XQ
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-- Ernesto Jiménez-Ruiz Lecturer in Artificial Intelligence
Department of Computer Science School of Science & Technology City, University of London https://www.city.ac.uk/people/academics/ernesto-jimenez-ruiz
— Reply to this email directly, view it on GitHub <https://github.com/FoodOntology/foodon/issues/6#issuecomment-1254668135 , or unsubscribe < https://github.com/notifications/unsubscribe-auth/AAMZGI7SB45A2DH33ZQZDVDV7QHADANCNFSM4CCZM3XQ
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-- Ernesto Jiménez-Ruiz Lecturer in Artificial Intelligence
Department of Computer Science School of Science & Technology City, University of London https://www.city.ac.uk/people/academics/ernesto-jimenez-ruiz
Agrovoc contains many concepts of interest, and portions could even be imported directly.
Naive search for concepts involving 'food' as either label syn or appearing in def (using https://github.com/cmungall/agrovoc-obo):