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From: BioPortal <ad...@bi...> - 2024-05-01 20:46:37
|
Relations Ontology (OBOREL) was processed for use in BioPortal. Here are the results: <br><br> Parsed successfully<br/>Indexed terms for search<br/>Indexed properties for search<br/>Class metrics calculated<br/>Created submission version diff successfully <br><br> Please contact su...@bi... if you have questions. <br><br> The ontology can be <a href="http://bioportal.bioontology.org/ontologies/OBOREL">browsed in BioPortal</a>. <br><br> Thank you,<br> The BioPortal Team |
From: BioPortal <ad...@bi...> - 2024-02-16 03:32:13
|
Relations Ontology (OBOREL) was processed for use in BioPortal. Here are the results: <br><br> Parsed successfully<br/>Indexed terms for search<br/>Indexed properties for search<br/>Class metrics calculated<br/>Created submission version diff successfully <br><br> Please contact su...@bi... if you have questions. <br><br> The ontology can be <a href="http://bioportal.bioontology.org/ontologies/OBOREL">browsed in BioPortal</a>. <br><br> Thank you,<br> The BioPortal Team |
From: Bill D. <wdd...@gm...> - 2024-02-09 14:39:29
|
Apologies for cross-posting. ---------- Dear Colleagues, Please help to distribute this Call for Papers. What: 15th International Conference on Biological and Biomedical Ontology (ICBO) The International Conference on Biological and Biomedical Ontology (ICBO) is a premier annual conference series that brings together researchers, students and professionals involved in the development and application of ontologies in all areas of biology, medicine, diseases, human health, genome biology, environment, biomes, nutrition, food, plants, agriculture and others. Together, they address issues pertaining to coordinated development of ontological resources, data standards, as well as the optimal use of ontologies in applications. ICBO 2024 website: https://icbo-conference.github.io/icbo2024/ Where and When: ICBO 2024 will be held together with the 14th International Conference on Formal Ontology in Information Systems (FOIS) in Enschede, The Netherlands, from 17-19 July 2024. Important Dates: Conference Dates: July 17th to July 19th 2024 Workshops/tutorials: July 17, 2024 Main conference: July 18 - July 19, 2024 Submission Dates: - workshops submissions: 15 March 2024. Notification 29 March 2024. - software demo submission (shared with FOIS): 17 April 2024. Notification: 15 May 2024. - ICBO conference papers submission: 26 March 2024. Notification 15 May 2024. - Journal Track submission deadline: continuous The unifying theme of ICBO 2024 is "Unifying Biological Knowledge: >From Molecules to Ecosystems". Submissions: - Submissions should be formatted according to the CEUR-ART template, single column (available from the conference website - Full papers: up to 12 pages - Short papers: up to 5 pages - Poster abstracts: 1 page, plus references - Submission link: https://cmt3.research.microsoft.com/ICBO2024/ Full submission details are available at https://icbo-conference.github.io/icbo2024/call/ |
From: <cj...@lb...> - 2021-04-06 17:41:26
|
Thanks everyone! We made great progress on the paper, almost there. If you weren't there, you may have been tagged on some things :-) On Monday, April 5, 2021 at 1:56:20 PM UTC-7 nlharris wrote: > Reminder that we have an RO meeting tomorrow, Tuesday April 5 (9am PT / 12 > noon ET / 17:00 UK). We will focus on the RO paper > <https://docs.google.com/document/d/1jzBDfMdepl9PL7ix6O-A4dej7qcihvu66kam9pUU-4U/edit> > . > > Description: > > Zoom: > https://lbnl.zoom.us/j/97163538233?pwd=czlTWTRzb0YvY0sxa1hwWERZUTFEQT09 > <https://www.google.com/url?q=https://lbnl.zoom.us/j/97163538233?pwd%3DczlTWTRzb0YvY0sxa1hwWERZUTFEQT09&sa=D&source=calendar&ust=1613148345504000&usg=AOvVaw0aDKnGL8cpkor7c87VwlpV> > > Rolling Agenda: http://bit.ly/ro-minutes (which is a shortcut for > https://docs.google.com/document/d/19dhzj5QoliQZQgDJRczI878rLtexzMDo1g0K9_LRUWk/edit# > ) > > Nomi > |
From: Alan R. <ala...@gm...> - 2020-05-04 22:19:59
|
The idea is to make a part-relation for each process/interval over which you want a transitive relation with simple inverse. If you want to say baby teeth part of human during childhood, then create the relations part-of-during-childhood, has-part-during-childhood. These are inverses and transitive (proofs available). (:forall (?x ?y) (:iff (part-of-during-childhood ?x ?y) (:forall (?t) (:implies (:forall (?tp) (:implies (ocurrent-part-of ?tp ?t) (participates-in ?x childhood-temporal-interval ?tp))) (continuant-part-of ?x ?y ?t)))))) You get inverse by changing continuant-part-of to has-continuant-part. Now if early-childhood is part of childhood, and we also define part-of-during-early-childhood. Then part-of-during-childhood implies part-of-during-early-childhood. What we can say in OWL: (inverse-object-properties part-of-during-childhood has-part-during-childhood) ditto for early-childhood (sub-object-property-of part-of-during-childhood part-of-during-early- childhood) (transitive-object-property part-of-during-childhood) ditto part-of-during-early-childhood (sub-object-property part-of-during-childhood continuant-part-of-at-some-times) ditto for has-part-during-early-childhood. You can do something similar but define it over a temporal interval, instead. If you are working in first order logic, then you add an axiom for each relation as above. part-of-at-all-times, framed from this perspective, is part-of-during-history-of. Pros: - Well-defined temporal relationship - 'symmetric' inverse - Works for non-rigid types Cons: - You have to create a bunch of part relations for the different life stages, and manage the subproperty relations yourself. OTOH you can query on part-of-at-some-time, so client doesn't have to worry about these if they don't want to. Alan Alan |
From: Ramona W. <rlw...@gm...> - 2019-07-30 15:44:31
|
For people who are at ICBO, we have a room reserved where we can do the RO call during lunch time. I don't know the room number, but it is on the second floor somewhere near the cafe. Ramona ------------------------------------------------------ Ramona L. Walls, Ph.D. Senior Scientific Analyst, CyVerse, University of Arizona Assistant Research Professor, Bio5 Institute, University of Arizona |
From: Bill H. <ho...@gm...> - 2019-02-28 01:27:03
|
We have a postdoctoral position open at the University of Florida, with an emphasis on ontology. More information, as well as an online application form, is available at: https://apply.interfolio.com/60592 >From the announcement: "A Postdoctoral Associate position is immediately available for highly ambitious, independent and motivated candidates to work in the University of Florida Biomedical Informatics program with an interdisciplinary research team. Barriers to linking, integrating, and efficiently exploiting health information impede the development of precision health. For example, different electronic health record (EHR) systems independently define structural data formats and encoding. Independent and heterogeneous data definitions pose challenges to interoperability of the data, e.g. merging data from different EHRs. Therefore, the effort required to integrate and link data is substantial. These challenges can be overcome by semantic interoperability via an ontology-driven data infrastructure. To accomplish semantic interoperability, the candidate will work with a group of experts in ontology, semantic web, data science, and biomedical informatics in general to harmonize." With apologies for cross-posting. |
From: Chris M. <cjm...@lb...> - 2019-02-12 01:48:38
|
Good catch - The OBO calendar entry doesn't say anything about RO, there's been no announcement on the RO list, and James is away, I say give this back to the OBO Editorial WG, and then let's do some prep before the next RO call. On Mon, Feb 11, 2019 at 9:32 AM Bjoern Peters <bp...@lj...> wrote: > I just saw on my calendar that we are having the OBO-operations / RO call > tomorrow (9-10 am Pacific time). Our goal was to follow up on the action > items from the workshop. We should absolutely do that, even though it looks > like we are under-prepared. > > What just came up today in the OBI call, what is the status of the > PATO:quality / BFO:quality re-alignment > https://github.com/oborel/obo-relations/pull/284 > > > > -- > 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 received this message because you are subscribed to the Google Groups > "obo-operations-committee" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to obo...@go.... > Visit this group at > https://groups.google.com/group/obo-operations-committee. > For more options, visit https://groups.google.com/d/optout. > |
From: Bjoern P. <bp...@lj...> - 2019-02-11 17:32:43
|
I just saw on my calendar that we are having the OBO-operations / RO call tomorrow (9-10 am Pacific time). Our goal was to follow up on the action items from the workshop. We should absolutely do that, even though it looks like we are under-prepared. What just came up today in the OBI call, what is the status of the PATO:quality / BFO:quality re-alignment https://github.com/oborel/obo-relations/pull/284 -- 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 |
From: Bill H. <ho...@gm...> - 2019-01-05 00:05:54
|
Join us for the Seventh Annual Meeting of the Clinical and Translation Science Ontology Working Group in Orlando, Florida, February 20-21, 2019. >From genomes to public health, newer and larger datasets are increasingly available to inform precision approaches to the treatment and prevention of disease and disorders. Managing these datasets--especially their integration--for everything from managing the opioid epidemic to the learning health system to translational science--requires more and better ontologies. This workshop will briefly survey the state-of-the-art in ontology at the nexus of these trends, identify needs and opportunities for future work and collaborations, and develop one or more white papers charting the course for the future, including a set of recommendations for key stakeholders. The Keynote Speaker is Janna Hastings, speaking on *Can ontologies help overcome the impasse in mental health research? *The meeting will also include a special session on ontologies in the area of opioid abuse. Details are here: http://ncorwiki.buffalo.edu/index.php/Ontology_for_Precision_Medicine:_From_Genomes_to_Public_Health |
From: <bp...@lj...> - 2018-11-21 01:14:39
|
Following the call today, I drafted a governance proposal here: https://docs.google.com/document/d/1ZsSxgY0gXfVdaylS9NjayGXm7u7535Y_I67Eu55cjL8/edit?usp=sharing Circulating it only on the OBO-relationships group for now. Please take a look and make suggestions / edits. If you want to significantly change any aspect of this (which I hope captures the spirit of our call today), please announce it here first instead, or create a new version of the document. - Bjoern |
From: Bill H. <ho...@gm...> - 2018-11-09 18:38:44
|
The Seventh Annual Meeting of the Clinical and Translation Science Ontology Working Group will take place in Orlando, Florida, February 20-21, 2019 Details are here <https://urldefense.proofpoint.com/v2/url?u=http-3A__ncorwiki.buffalo.edu_index.php_Ontology-5Ffor-5FPrecision-5FMedicine-3A-5FFrom-5FGenomes-5Fto-5FPublic-5FHealth&d=DwMFaQ&c=pZJPUDQ3SB9JplYbifm4nt2lEVG5pWx2KikqINpWlZM&r=SP8lV1H3Lge3YTiRfk_DQw&m=FaN53GauQUfwOxVtTkZxddJcv2gAwBVxjr0XC-U-ae0&s=iXqC_iNy2ZX_WcPP6ZeaX72ixPJSSnOm7ALuW0WG--Q&e=> Please distribute widely. The meeting will include a special session on ontologies in the area of opioid abuse. The Keynote Speaker is Janna Hastings. Please write to Bill Hogan ho...@uf... if you are interested in participating With apologies for cross posting... |
From: <cjm...@lb...> - 2018-11-09 15:33:01
|
On Wednesday, November 7, 2018 at 8:40:52 PM UTC-8, Bill Duncan wrote: > > I agree with Melissa with the caveat that the ambiguities in the NCIT need > to be cleared up. If you read the definitions of the terms under the NCIT > neoplasm branch, it is clear (in most, perhaps all cases) that the terms > denote material entities, not disposositions. > I would be very careful about making assumptions of ontological commitment from reading text definitions aimed at ordinary non-ontologists. There may be an implicit conflation there that most people are comfortable with, whereas we seek to name entities for each aspect of the concept. The definition of neoplasm does indeed read as if it were a ME, but there are syndromes placed there, e.g. is_a NCIT:C3262 ! Neoplasm is_a NCIT:C7062 ! Neoplasm by Special Category is_a NCIT:C9305 ! Malignant Neoplasm is_a NCIT:C9479 ! Hereditary Malignant Neoplasm is_a NCIT:C120083 ! Hereditary Nonpolyposis Colorectal Cancer is_a NCIT:C8494 ! Lynch Syndrome *** Also placed here: is_a NCIT:C2991 ! Disease or Disorder is_a NCIT:C28193 ! Syndrome is_a NCIT:C54705 ! Neoplastic Syndrome is_a NCIT:C3266 ! Hereditary Neoplastic Syndrome is_a NCIT:C120083 ! Hereditary Nonpolyposis Colorectal Cancer is_a NCIT:C8494 ! Lynch Syndrome *** is_a NCIT:C3101 ! Genetic Disorder is_a NCIT:C3266 ! Hereditary Neoplastic Syndrome is_a NCIT:C120083 ! Hereditary Nonpolyposis Colorectal Cancer is_a NCIT:C8494 ! Lynch Syndrome *** is_a NCIT:C7757 ! DNA Repair Disorder is_a NCIT:C8494 ! Lynch Syndrome *** > My only contention with NCIT neoplasm branch is that the structure needs > to be explicit about this. Plus, there is the issue of how you integrate > NCIT with other ontologies that define cancer as a disposition. > > That being said, there are a number of other parts of the NCIT that do > need work. For example, the cell, processual, and genomic underpinnings of > cancer, and the relations between these entities. I think these latter > areas are what we should focus on, in my humble opinion. > Yes. I assume the main reason these have not received much attention in NCIT is that they have primarily been used for axiomatizing the neoplasm branch, and the vast majority of the use cases pertain to the neoplasm branch and not the ancillary ones. > > Bill > > On Wed, Nov 7, 2018 at 10:50 PM Suzanna Lewis <se...@lb...> wrote: > >> +1 to Melissa's comment >> >> See this for a reality check - >> https://xkcd.com/927/ >> >> On Thu, Nov 8, 2018 at 11:48 AM Melissa Haendel <me...@ti...> >> wrote: >> >>> Hi all, >>> >>> Given that there have, AFAIK, been no requests made to try to improve >>> modeling of NCIT on the tracker, and conversely, collaborative effort has >>> been ongoing on part of multiple OBO-ists and NCI to start to make NCIT >>> more OBO-model compliant, I would think it would be consistent with our >>> values to work towards orthologonality and improvement rather than building >>> a new ontology. There is an incredible amount of domain knowledge modeling >>> within NCIT that have taken many ontologists and domain experts decades to >>> build. Further, NCI is quite amenable to feedback and is very >>> collaborative. We even got them to have the license updated to CC BY 4.0 >>> recently in order to be compliant with OBO standards. >>> >>> My two cents. >>> Melissa >>> >>> >>> >>> >>> On Nov 7, 2018, at 7:30 PM, <wce...@gm...> <wce...@gm...> >>> wrote: >>> >>> Bill, >>> >>> I am 100% with you on this one. Both I and Stefan Schulz have shown that >>> the NCIT is very badly designed and isn’t worth to take as a basis for an >>> ontology. But building a good ontology, and then express NCIT in terms of >>> that good ontology – thereby of course marking the errors and ambiguities >>> in NCIT – is a worthwhile enterprise. >>> >>> W >>> >>> *From:* Bill Duncan <wdd...@gm...> >>> *Sent:* Wednesday, November 07, 2018 5:51 PM >>> *To:* obo...@go... >>> *Subject:* Re: RO funding... >>> >>> The lack of ontological commitment is the reason why I am developing the >>> neoplasm ontology (which has been stalled lately, unfortunately). For >>> instance, when modeling pathology data, we need to be able to distinguish >>> between the material entity that the pathologist examines and other >>> findings. >>> >>> On Wed, Nov 7, 2018 at 2:36 PM Melissa Haendel <me...@ti...> >>> wrote: >>> >>>> I would second that…. I’ve been on the ITCR panel and I must say I >>>> think it is an odd choice for an OBO/RO application. Also, efforts to make >>>> to help make the NCIT OBO compatible >>>> <https://medium.com/@MonarchInit/tailoring-the-nci-thesaurus-for-semantic-interoperability-21305ccfe3a6> >>>> (recognizing that there is much more to do) have been underway, I think it >>>> would probably not go over well on ITCR to propose an alternative cancer >>>> terminology, especially where NCIT is the de facto standard for the >>>> regulatory bodies. >>>> >>>> On Nov 7, 2018, at 11:33 AM, Chris Mungall <cmu...@gm...> wrote: >>>> >>>> This is correct, NCIT is ontologically not fully committed to OBO upper >>>> level classes. This doesn't seem like a great reason for making an entirely >>>> new ontology though, there are techniques for leveraging the decades of >>>> expert work that has gone into NCIT (there is a paper by Stafan Schulz, >>>> will find it later). I know OBO people like to focus on the upper levels >>>> but take a look at the depth and axiomatization in the neoplasm branch of >>>> NCIT there is a lot there. Also for an NCI application it would be wise to >>>> be aware of these things. >>>> On 7 Nov 2018, at 10:05, Bill Duncan wrote: >>>> >>>> Hi Jim. Yes, you are correct. We define neoplasm as being a type of >>>> material entity. This distinguishes it from the disease ontology. As for >>>> whether a neoplasm is a phenotype, it depends (I guess) on how you define >>>> 'phenotype'. Perhaps neoplasms are both material entities and phenotypes? >>>> At first pass, this sounds reasonable to me, but asserted polyhierachies >>>> are frowned upon by some (maybe most). >>>> >>>> Bill >>>> >>>> On Wed, Nov 7, 2018 at 12:06 PM Jim Balhoff <ba...@re...> wrote: >>>> >>>>> I’m sure Bill or Alex can say more, but one of the issues they >>>>> presented at ICBO was the ambiguity of whether a neoplasm is being defined >>>>> as a material entity or a disease or phenotype. >>>>> >>>>> >>>>> On Nov 7, 2018, at 12:03 PM, Chris Mungall <cmu...@gm...> wrote: >>>>> >>>>> This is getting outside the realm of RO, but how does the neoplasm >>>>> ontology differ from what is in the NCIT ontology? >>>>> http://purl.obolibrary.org/obo/NCIT_C3262 >>>>> On 7 Nov 2018, at 4:58, Judith wrote: >>>>> >>>>> Sounds like great stuff to integrate into an NCI proposal. Welcome >>>>> aboard Bill >>>>> >>>>> Judy >>>>> >>>>> Sent from my iPhone >>>>> >>>>> On Nov 6, 2018, at 8:27 PM, Bill Duncan <wdd...@gm...> wrote: >>>>> >>>>> Hi all >>>>> >>>>> If possible, I would like to be a part of this. I am currently working >>>>> on a neoplasm ontology and I have access to my institute's Cancer Registry >>>>> database as well as a number of custom research databases developed for >>>>> prostate, gyn, head and neck, and lung cancer (and more). >>>>> >>>>> I am also developing a a triple store to house genomic clinical panels >>>>> integrated with the above mentioned data sources. >>>>> >>>>> Bill >>>>> >>>>> >>>>> On Tue, Nov 6, 2018 at 12:51 PM Bjoern Peters <bp...@lj...> wrote: >>>>> >>>>>> Thanks for the update Judy, that makes perfect sense. >>>>>> >>>>>> - Bjoern >>>>>> >>>>>> On Tue, Nov 6, 2018 at 9:46 AM Judith Blake <Jud...@ja...> >>>>>> wrote: >>>>>> >>>>>>> Hi Darren and Bjoern, >>>>>>> >>>>>>> I’m following up on discussions about RO funding at the Denver >>>>>>> meeting where you mentioned you are interested in helping with writing a >>>>>>> grant to fund RO - Here’s where things are now. >>>>>>> >>>>>>> Chris S, Larry and I talked last week with Juli Klemm (NCI) about >>>>>>> NCI ITCR funding options. The RFA for the option best for RO --- *NCI >>>>>>> ITCR PAR-15-331 ----* runs out shortly, but she said - good >>>>>>> prospects for renewal of the program. We should hear more about that in >>>>>>> Dec. >>>>>>> >>>>>>> In the meantime, we started a google doc to capture thoughts about >>>>>>> aims and projects to consider. Once there is a solid funding mechanism, we >>>>>>> can refine this. >>>>>>> >>>>>>> Here’s the link to the google doc. Things are on hold for the >>>>>>> moment….we will continue working on this project in Dec…. >>>>>>> >>>>>>> >>>>>>> https://docs.google.com/document/d/1EM7bvsn3KWnUEmjeq6rjFfjXXSmK3u2uHfNk_AZHN3o/edit?usp=sharing >>>>>>> >>>>>>> >>>>>>> Best >>>>>>> >>>>>>> Judy >>>>>>> >>>>>>> *Professor Judith A Blake* >>>>>>> *Bioinformatics and Computatonal Biology* >>>>>>> *The Jackson Laboratory* >>>>>>> *Bar Harbor, ME 04609* >>>>>>> *1-207-288-6248 * >>>>>>> >>>>>>> -- >>>>>>> >>>>>>> --- >>>>>>> >>>>>>> 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. >>>>>>> >>>>>> >>>>>> >>>>>> -- >>>>>> Bjoern Peters >>>>>> Professor >>>>>> La Jolla Institute for Allergy and Immunology >>>>>> 9420 Athena Circle >>>>>> <https://maps.google.com/?q=9420+%0D%0A++++++++++++++++Athena+Circle+La+%0D%0A++++++++++++++++Jolla,+CA+92037,+USA&entry=gmail&source=g> >>>>>> La Jolla, CA 92037, USA >>>>>> <https://maps.google.com/?q=9420+%0D%0A++++++++++++++++Athena+Circle+La+%0D%0A++++++++++++++++Jolla,+CA+92037,+USA&entry=gmail&source=g> >>>>>> Tel: 858/752-6914 >>>>>> Fax: 858/752-6987 >>>>>> http://www.liai.org/pages/faculty-peters >>>>>> >>>>>> -- >>>>>> You received this message because you are subscribed to the Google >>>>>> Groups "obo-relations" group. >>>>>> To unsubscribe from this group and stop receiving emails from it, >>>>>> send an email to obo...@go.... >>>>>> To post to this group, send email to obo...@go.... >>>>>> Visit this group at https://groups.google.com/group/obo-relations. >>>>>> For more options, visit https://groups.google.com/d/optout. >>>>>> >>>>> >>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "obo-relations" group. >>>>> To unsubscribe from this group and stop receiving emails from it, send >>>>> an email to obo...@go.... >>>>> To post to this group, send email to obo...@go.... >>>>> Visit this group at https://groups.google.com/group/obo-relations. >>>>> For more options, visit https://groups.google.com/d/optout. >>>>> >>>>> >>>>> -- >>>>> You received this message because you are subscribed to the Google >>>>> Groups "obo-relations" group. >>>>> To unsubscribe from this group and stop receiving emails from it, send >>>>> an email to obo...@go.... >>>>> To post to this group, send email to obo...@go.... >>>>> Visit this group at https://groups.google.com/group/obo-relations. >>>>> For more options, visit 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Excuse the typos > |
From: Barry S. <if...@gm...> - 2018-11-08 18:10:02
|
Please replace this item in my last post You define 'causally downstream of or within' as 'inverse of causally upstream of or within'. However (perhaps, again, depending on what you mean by 'within') the inverse of causally upstream of or within would be: 'EITHER causally downstream of and within OR causally downstream of and not within OR causally upstream of and not within OR causally neither upstream of nor downstream of [e.g. because simultaneous with] and so on ... with this: You define 'causally downstream of or within' as 'inverse of causally > upstream of or within'. However (perhaps, again, depending on what you mean > by 'within') defining the inverse of 'causally upstream of or within', > however, should surely take account of the fact that the inverse of > 'within' is not 'within' (if A is within B then B is within A only if A and > B are identical) > |
From: Barry S. <if...@gm...> - 2018-11-08 16:55:40
|
*definition <https://www.ebi.ac.uk/ols/search?q=definition&exact=true&type=property&ontology=ro>* p 'causally upstream or within' q iff (1) the end of p is before the end of q and (2) the execution of p exerts some causal influence over the outputs of q; i.e. if p was abolished or the outputs of p were to be modified, this would necessarily affect q. *editor note <https://www.ebi.ac.uk/ols/search?q=editor%20note&exact=true&type=property&ontology=ro>* We would like to make this disjoint with 'preceded by', but this is prohibited in OWL2 The definition is somewhat problematic for a number of reasons: 'within' is not defined. you say 'exerts some causal influence over the outputs of q'; but this would be satisfied where p, via some path completely independent of q, exerts some causal influence on one of q's outputs In (2) why not just say" 'exerts some causal influence on q' Why do you want this to be disjoint from 'precedes'? You say 'the execution of p exerts some causal influence' -- instead of 'the execution of p' why not just say 'p'? execution surely applies to functions, not to processes. Processes just occur. You say that clause (2) is synonymous with: if p was abolished or the outputs of p were to be modified, this would necessarily affect q. But again, surely many of the outputs of p might come to be modified long after q has already occurred and so could not affect q at all. You define 'causally downstream of or within' as 'inverse of causally upstream of or within'. However (perhaps, again, depending on what you mean by 'within') the inverse of causally upstream of or within would be: 'EITHER causally downstream of and within OR causally downstream of and not within OR causally upstream of and not within OR causally neither upstream of nor downstream of [e.g. because simultaneous with] and so on ... Incidentally, it would be nice to get rid of 'within' entirely, if at all possible, because then in all the comma expressions (such as 'causally upstream of, positive effect') the comma could elegantly (and logically usefully) be replaced by 'with' BS |
From: Jie Z. <zhe...@gm...> - 2018-11-05 16:29:15
|
What's the domain and range of the RO: "inheres in" (RO:0000052)? In the RO ontology, "inheres in" has four subProperties which are: - function of - quality of - role of - disposition of So, I think its domain is "specifically dependent continuant" including both quality and 'realizable entity' (disposition and role). Based on BFO, I think its range is "independent continuant". I can understand current changes want to change the range to something like "independent continuant" or "process". So, it will allow to associate "quality" with "process". My question is whether we'd like to make the relation also apply to 'realizable entity' like disposition and role or only to quality. Current "realized in" relation is used to associate 'realizable entity' with process. If we just relabel the RO: "inheres in" (RO:0000052) and changed the range to "independent continuant" or "process", does it mean RO: "realized in" (BFO_0000054) is a subProperty of RO: "characteristic of"? If not, what's difference between a 'realizable entity' 'realized in' a process and a 'realizable entity' 'characteristic of' a process? Thanks, Jie On Thursday, October 25, 2018 at 1:36:33 PM UTC-4, Chris Mungall wrote: > > At the RO meeting with other RO developers. > > There will be a pull request on RO shortly that will relabel "inheres in" ( > RO:0000052) to "characteristic of" (and also > bearer_of->has_characteristic, and also change to inheres_in_part_of). > We're open to other strings, but the crucial point is that this reflects > that this relation is used for something more general than the string BFO > sense of inheres_in (which forbids process qualities). > > More later... > |
From: Damion D. <dam...@gm...> - 2018-10-25 19:35:50
|
So we'd express "mass 'characteristic of' some organism" rather than "mass 'inheres in' some organism". And more centrally, "organism 'has characteristic' some mass" (as all material entities do, unless one includes photons and gluons?) rather than 'organism 'bearer of' some mass". 'material entity' could be enhanced in intermediate ontology to have "material entity 'has characteristic' some mass"? Can you give an example of a process quality? Are those all ICE constructs like speed of reaction? |
From: <cjm...@lb...> - 2018-10-20 21:00:53
|
New release is out. Release notes here: https://github.com/oborel/obo-relations/releases/tag/v2018-10-19 The complete list of release files is listed on the RO OBO page: http://obofoundry.org/ontology/ro.html I expect the ontology will be visible on OLS on Monday, and Ontobee at some point in the future. Note that with RO (more so than most other ontologies), Protege is recommended to see a complete account of all axioms and axiom annotations. On Sunday, October 14, 2018 at 4:13:22 PM UTC-7, Chris Mungall wrote: > > I intend to publish a new version before the RO meeting later this month > > There is a pre-release here: > https://github.com/oborel/obo-relations/releases/tag/v2018-09-25-PRELEASE > > And one PR to be merged: > https://github.com/oborel/obo-relations/pull/261 > > This PR contains stronger domain and range constraints for various > relations. It is possible that this will have knock-on effects of rendering > classes that use these unsatisfiable. Unfortunately we don't have a readily > plumbed-in of checking this en-masse across OBO at the moment. > > Full diff below (this should render as html in your mail program): > Original Ontology > > - IRI: http://purl.obolibrary.org/obo/ro.owl > - VersionIRI: > http://purl.obolibrary.org/obo/ro/releases/2018-05-11/ro.owl > > New Ontology > > - IRI: http://purl.obolibrary.org/obo/ro.owl > - VersionIRI: > http://purl.obolibrary.org/obo/ro/releases/2018-10-01/ro.owl > > Report for classes Class objects lost from source: 10 > > - branchiness <http://purl.obolibrary.org/obo/PATO_0002009> > - morphology <http://purl.obolibrary.org/obo/PATO_0000051> > - shape <http://purl.obolibrary.org/obo/PATO_0000052> > - biome <http://purl.obolibrary.org/obo/ENVO_00000428> > - cell part <http://purl.obolibrary.org/obo/CARO_0000014> > - disposition <http://purl.obolibrary.org/obo/BFO_0000016> > - quality <http://purl.obolibrary.org/obo/PATO_0000001> > - connected anatomical system > <http://purl.obolibrary.org/obo/CARO_0000011> > - multi-cell-part structure > <http://purl.obolibrary.org/obo/CARO_0001000> > - null <http://purl.obolibrary.org/obo/GO_0005515> > > Class objects new in target: 4 New Class : generically dependent > continuant <http://purl.obolibrary.org/obo/BFO_0000031> > > - generically dependent continuant > <http://purl.obolibrary.org/obo/BFO_0000031> *definition > <http://purl.obolibrary.org/obo/IAO_0000115>* A continuant that is > dependent on one or other independent continuant bearers. For every > instance of A requires some instance of (an independent continuant type) B > but which instance of B serves can change from time to time. > - generically dependent continuant > <http://purl.obolibrary.org/obo/BFO_0000031> *SubClassOf* continuant > <http://purl.obolibrary.org/obo/BFO_0000002> > - DisjointClasses( independent continuant > <http://purl.obolibrary.org/obo/BFO_0000004> generically dependent > continuant <http://purl.obolibrary.org/obo/BFO_0000031> ) > - DisjointClasses( specifically dependent continuant > <http://purl.obolibrary.org/obo/BFO_0000020> generically dependent > continuant <http://purl.obolibrary.org/obo/BFO_0000031> ) > - generically dependent continuant > <http://purl.obolibrary.org/obo/BFO_0000031> *label > <http://www.w3.org/2000/01/rdf-schema#label>* generically dependent > continuant > > New Class : organism or virus or viroid > <http://purl.obolibrary.org/obo/CARO_0001010> > > - organism or virus or viroid > <http://purl.obolibrary.org/obo/CARO_0001010> *SubClassOf* material > entity <http://purl.obolibrary.org/obo/BFO_0000040> > - organism or virus or viroid > <http://purl.obolibrary.org/obo/CARO_0001010> *label > <http://www.w3.org/2000/01/rdf-schema#label>* organism or virus or > viroid > > New Class : disease <http://purl.obolibrary.org/obo/OGMS_0000031> > > - disease <http://purl.obolibrary.org/obo/OGMS_0000031> *label > <http://www.w3.org/2000/01/rdf-schema#label>* disease > - disease <http://purl.obolibrary.org/obo/OGMS_0000031> *SubClassOf* > disposition <http://purl.obolibrary.org/obo/BFO_0000016> > - disease <http://purl.obolibrary.org/obo/OGMS_0000031> *definition > <http://purl.obolibrary.org/obo/IAO_0000115>* A disposition (i) to > undergo pathological processes that (ii) exists in an organism because of > one or more disorders in that organism. > > New Class : phenotype <http://purl.obolibrary.org/obo/UPHENO_0001001> > > - phenotype <http://purl.obolibrary.org/obo/UPHENO_0001001> > *SubClassOf* quality <http://purl.obolibrary.org/obo/PATO_0000001> > - phenotype <http://purl.obolibrary.org/obo/UPHENO_0001001> *label > <http://www.w3.org/2000/01/rdf-schema#label>* phenotype > > Changed Class objects: 5 Changes for: material anatomical entity > <http://purl.obolibrary.org/obo/CARO_0000006> > > - *Added* > - *+* material anatomical entity > <http://purl.obolibrary.org/obo/CARO_0000006> *SubClassOf* > ObjectAllValuesFrom( drains > <http://purl.obolibrary.org/obo/RO_0002179> anatomical structure > <http://purl.obolibrary.org/obo/CARO_0000003> ) > > Changes for: occurrent <http://purl.obolibrary.org/obo/BFO_0000003> > > - *Added* > - *+* occurrent <http://purl.obolibrary.org/obo/BFO_0000003> > *SubClassOf* ObjectAllValuesFrom( in similarity relationship with > <http://purl.obolibrary.org/obo/RO_HOM0000000> occurrent > <http://purl.obolibrary.org/obo/BFO_0000003> ) > > Changes for: null <http://purl.obolibrary.org/obo/GO_0004872> > > - *Deleted* > - *-* receptor activity <http://purl.obolibrary.org/obo/GO_0004872> *label > <http://www.w3.org/2000/01/rdf-schema#label>* receptor activity > > Changes for: process <http://purl.obolibrary.org/obo/BFO_0000015> > > - *Added* > - *+* process <http://purl.obolibrary.org/obo/BFO_0000015> > *SubClassOf* ObjectAllValuesFrom( has prototype > <http://purl.obolibrary.org/obo/RO_0002214> process > <http://purl.obolibrary.org/obo/BFO_0000015> ) > > Changes for: continuant <http://purl.obolibrary.org/obo/BFO_0000002> > > - *Added* > - *+* continuant <http://purl.obolibrary.org/obo/BFO_0000002> > *SubClassOf* ObjectAllValuesFrom( has prototype > <http://purl.obolibrary.org/obo/RO_0002214> continuant > <http://purl.obolibrary.org/obo/BFO_0000002> ) > - *+* continuant <http://purl.obolibrary.org/obo/BFO_0000002> > *SubClassOf* ObjectAllValuesFrom( in similarity relationship with > <http://purl.obolibrary.org/obo/RO_HOM0000000> continuant > <http://purl.obolibrary.org/obo/BFO_0000002> ) > > Report for properties ObjectProperty objects lost from source: 1 > > - has role <http://purl.obolibrary.org/obo/RO_0000087> > > ObjectProperty objects new in target: 7 New ObjectProperty : has > anatomical participant <http://purl.obolibrary.org/obo/RO_0040036> > > - ObjectPropertyRange( has anatomical participant > <http://purl.obolibrary.org/obo/RO_0040036> material anatomical entity > <http://purl.obolibrary.org/obo/CARO_0000006> *or* immaterial > anatomical entity <http://purl.obolibrary.org/obo/CARO_0000007> ) > - has anatomical participant > <http://purl.obolibrary.org/obo/RO_0040036> *creation date > <http://www.geneontology.org/formats/oboInOwl#creation_date>* > 2018-09-26T01:08:58Z > - has anatomical participant > <http://purl.obolibrary.org/obo/RO_0040036> *definition > <http://purl.obolibrary.org/obo/IAO_0000115>* p has anatomical > participant c iff p has participant c, and c is an anatomical entity > - SubObjectPropertyOf( has anatomical participant > <http://purl.obolibrary.org/obo/RO_0040036> has participant > <http://purl.obolibrary.org/obo/RO_0000057> ) > - has anatomical participant > <http://purl.obolibrary.org/obo/RO_0040036> *label > <http://www.w3.org/2000/01/rdf-schema#label>* has anatomical > participant > - has anatomical participant > <http://purl.obolibrary.org/obo/RO_0040036> *created by > <http://www.geneontology.org/formats/oboInOwl#created_by>* cjm > > New ObjectProperty : disease relationship > <http://purl.obolibrary.org/obo/RO_0040035> > > - disease relationship <http://purl.obolibrary.org/obo/RO_0040035> *created > by <http://www.geneontology.org/formats/oboInOwl#created_by>* cjm > - disease relationship <http://purl.obolibrary.org/obo/RO_0040035> *creation > date <http://www.geneontology.org/formats/oboInOwl#creation_date>* > 2018-09-26T00:00:32Z > - disease relationship <http://purl.obolibrary.org/obo/RO_0040035> *label > <http://www.w3.org/2000/01/rdf-schema#label>* disease relationship > - disease relationship <http://purl.obolibrary.org/obo/RO_0040035> *definition > <http://purl.obolibrary.org/obo/IAO_0000115>* This relation groups > relations between diseases and any other kind of entity. > - disease relationship <http://purl.obolibrary.org/obo/RO_0040035> *curator > note <http://purl.obolibrary.org/obo/IAO_0000232>* Do not use this > relation directly. It is intended as a grouping for a diverse set of > relations, in which the subject or object is a disease. > > New ObjectProperty : in similarity relationship with > <http://purl.obolibrary.org/obo/RO_HOM0000000> > > - in similarity relationship with > <http://purl.obolibrary.org/obo/RO_HOM0000000> *database cross > reference <http://www.geneontology.org/formats/oboInOwl#hasDbXref>* > ECO:0000041 > - in similarity relationship with > <http://purl.obolibrary.org/obo/RO_HOM0000000> *definition > <http://purl.obolibrary.org/obo/IAO_0000115>* Relation between > biological objects that resemble or are related to each other sufficiently > to warrant a comparison. { database cross reference > <http://www.geneontology.org/formats/oboInOwl#hasDbXref>= > http://purl.obolibrary.org/obo/HOM_0000000 , database cross reference > <http://www.geneontology.org/formats/oboInOwl#hasDbXref>=BGEE:curator > } > - in similarity relationship with > <http://purl.obolibrary.org/obo/RO_HOM0000000> *http://purl.org/dc/elements/1.1/creator > <http://purl.org/dc/elements/1.1/creator>* http://bgee.unil.ch > - in similarity relationship with > <http://purl.obolibrary.org/obo/RO_HOM0000000> *has exact synonym > <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym>* > sameness > - in similarity relationship with > <http://purl.obolibrary.org/obo/RO_HOM0000000> *database cross > reference <http://www.geneontology.org/formats/oboInOwl#hasDbXref>* > SO:similar_to > - in similarity relationship with > <http://purl.obolibrary.org/obo/RO_HOM0000000> *has exact synonym > <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym>* > similar to > - in similarity relationship with > <http://purl.obolibrary.org/obo/RO_HOM0000000> *seeAlso > <http://www.w3.org/2000/01/rdf-schema#seeAlso>* > http://purl.obolibrary.org/obo/HOM_0000000 > - in similarity relationship with > <http://purl.obolibrary.org/obo/RO_HOM0000000> *label > <http://www.w3.org/2000/01/rdf-schema#label>* in similarity > relationship with > - SymmetricObjectProperty( in similarity relationship with > <http://purl.obolibrary.org/obo/RO_HOM0000000> ) > - in similarity relationship with > <http://purl.obolibrary.org/obo/RO_HOM0000000> *has related synonym > <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym>* > resemblance > - in similarity relationship with > <http://purl.obolibrary.org/obo/RO_HOM0000000> *has related synonym > <http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym>* > correspondence { database cross reference > <http://www.geneontology.org/formats/oboInOwl#hasDbXref>= > http://dx.doi.org/10.1007/BF02814479 } > - in similarity relationship with > <http://purl.obolibrary.org/obo/RO_HOM0000000> *http://purl.org/dc/elements/1.1/source > <http://purl.org/dc/elements/1.1/source>* > http://www.ncbi.nlm.nih.gov/pubmed/20116127 > > New ObjectProperty : is concretized as > <http://purl.obolibrary.org/obo/RO_0000058> > > - is concretized as <http://purl.obolibrary.org/obo/RO_0000058> *definition > <http://purl.obolibrary.org/obo/IAO_0000115>* A relationship between a > generically dependent continuant and a specifically dependent continuant, > in which the generically dependent continuant depends on some independent > continuant in virtue of the fact that the specifically dependent continuant > also depends on that same independent continuant. A generically dependent > continuant may be concretized as multiple specifically dependent > continuants. > - is concretized as <http://purl.obolibrary.org/obo/RO_0000058> *example > of usage <http://purl.obolibrary.org/obo/IAO_0000112>* A journal > article is an information artifact that inheres in some number of printed > journals. For each copy of the printed journal there is some quality that > carries the journal article, such as a pattern of ink. The journal article > (a generically dependent continuant) is concretized as the quality (a > specifically dependent continuant), and both depend on that copy of the > printed journal (an independent continuant). > - ObjectPropertyRange( is concretized as > <http://purl.obolibrary.org/obo/RO_0000058> specifically dependent > continuant <http://purl.obolibrary.org/obo/BFO_0000020> ) > - is concretized as <http://purl.obolibrary.org/obo/RO_0000058> *example > of usage <http://purl.obolibrary.org/obo/IAO_0000112>* An investigator > reads a protocol and forms a plan to carry out an assay. The plan is a > realizable entity (a specifically dependent continuant) that concretizes > the protocol (a generically dependent continuant), and both depend on the > investigator (an independent continuant). The plan is then realized by the > assay (a process). > - InverseObjectProperties( is concretized as > <http://purl.obolibrary.org/obo/RO_0000058> concretizes > <http://purl.obolibrary.org/obo/RO_0000059> ) > - ObjectPropertyDomain( is concretized as > <http://purl.obolibrary.org/obo/RO_0000058> generically dependent > continuant <http://purl.obolibrary.org/obo/BFO_0000031> ) > - is concretized as <http://purl.obolibrary.org/obo/RO_0000058> *label > <http://www.w3.org/2000/01/rdf-schema#label>* is concretized as > > New ObjectProperty : concretizes > <http://purl.obolibrary.org/obo/RO_0000059> > > - concretizes <http://purl.obolibrary.org/obo/RO_0000059> *example of > usage <http://purl.obolibrary.org/obo/IAO_0000112>* A journal article > is an information artifact that inheres in some number of printed journals. > For each copy of the printed journal there is some quality that carries the > journal article, such as a pattern of ink. The quality (a specifically > dependent continuant) concretizes the journal article (a generically > dependent continuant), and both depend on that copy of the printed journal > (an independent continuant). > - concretizes <http://purl.obolibrary.org/obo/RO_0000059> *definition > <http://purl.obolibrary.org/obo/IAO_0000115>* A relationship between a > specifically dependent continuant and a generically dependent continuant, > in which the generically dependent continuant depends on some independent > continuant in virtue of the fact that the specifically dependent continuant > also depends on that same independent continuant. Multiple specifically > dependent continuants can concretize the same generically dependent > continuant. > - ObjectPropertyDomain( concretizes > <http://purl.obolibrary.org/obo/RO_0000059> specifically dependent > continuant <http://purl.obolibrary.org/obo/BFO_0000020> ) > - concretizes <http://purl.obolibrary.org/obo/RO_0000059> *example of > usage <http://purl.obolibrary.org/obo/IAO_0000112>* An investigator > reads a protocol and forms a plan to carry out an assay. The plan is a > realizable entity (a specifically dependent continuant) that concretizes > the protocol (a generically dependent continuant), and both depend on the > investigator (an independent continuant). The plan is then realized by the > assay (a process). > - concretizes <http://purl.obolibrary.org/obo/RO_0000059> *label > <http://www.w3.org/2000/01/rdf-schema#label>* concretizes > - InverseObjectProperties( is concretized as > <http://purl.obolibrary.org/obo/RO_0000058> concretizes > <http://purl.obolibrary.org/obo/RO_0000059> ) > - ObjectPropertyRange( concretizes > <http://purl.obolibrary.org/obo/RO_0000059> generically dependent > continuant <http://purl.obolibrary.org/obo/BFO_0000031> ) > > New ObjectProperty : generically depends on > <http://purl.obolibrary.org/obo/RO_0010001> > > - ObjectPropertyRange( generically depends on > <http://purl.obolibrary.org/obo/RO_0010001> independent continuant > <http://purl.obolibrary.org/obo/BFO_0000004> ) > - generically depends on <http://purl.obolibrary.org/obo/RO_0010001> *example > of usage <http://purl.obolibrary.org/obo/IAO_0000112>* The novel *War > and Peace* generically depends on this copy of the novel. > - generically depends on <http://purl.obolibrary.org/obo/RO_0010001> *label > <http://www.w3.org/2000/01/rdf-schema#label>* generically depends on > - generically depends on <http://purl.obolibrary.org/obo/RO_0010001> *example > of usage <http://purl.obolibrary.org/obo/IAO_0000112>* The score of a > symphony g-depends on a copy of the score. > - generically depends on <http://purl.obolibrary.org/obo/RO_0010001> *definition > source <http://purl.obolibrary.org/obo/IAO_0000119>* [072-ISO] > - generically depends on <http://purl.obolibrary.org/obo/RO_0010001> *example > of usage <http://purl.obolibrary.org/obo/IAO_0000112>* This pdf file > generically depends on this server. > - InverseObjectProperties( generically depends on > <http://purl.obolibrary.org/obo/RO_0010001> is carrier of > <http://purl.obolibrary.org/obo/RO_0010002> ) > - generically depends on <http://purl.obolibrary.org/obo/RO_0010001> *example > of usage <http://purl.obolibrary.org/obo/IAO_0000112>* The pattern > shared by chess boards generically depends on any chess board. > - ObjectPropertyDomain( generically depends on > <http://purl.obolibrary.org/obo/RO_0010001> generically dependent > continuant <http://purl.obolibrary.org/obo/BFO_0000031> ) > - generically depends on <http://purl.obolibrary.org/obo/RO_0010001> *example > of usage <http://purl.obolibrary.org/obo/IAO_0000112>* Genetic > information generically depend on molecules of DNA. > - generically depends on <http://purl.obolibrary.org/obo/RO_0010001> *definition > <http://purl.obolibrary.org/obo/IAO_0000115>* A generically dependent > continuant *b* generically depends on an independent continuant *c* at > time *t* means: there inheres in *c* a specifically deendent > continuant which concretizes *b* at *t*. > - generically depends on <http://purl.obolibrary.org/obo/RO_0010001> *has > exact synonym > <http://www.geneontology.org/formats/oboInOwl#hasExactSynonym>* > g-depends on > > New ObjectProperty : is carrier of > <http://purl.obolibrary.org/obo/RO_0010002> > > - is carrier of <http://purl.obolibrary.org/obo/RO_0010002> *definition > source <http://purl.obolibrary.org/obo/IAO_0000119>* [072-ISO] > - is carrier of <http://purl.obolibrary.org/obo/RO_0010002> *example > of usage <http://purl.obolibrary.org/obo/IAO_0000112>* This hard drive > is carrier of these data items. > - is carrier of <http://purl.obolibrary.org/obo/RO_0010002> *label > <http://www.w3.org/2000/01/rdf-schema#label>* is carrier of > - ObjectPropertyDomain( is carrier of > <http://purl.obolibrary.org/obo/RO_0010002> independent continuant > <http://purl.obolibrary.org/obo/BFO_0000004> ) > - InverseObjectProperties( generically depends on > <http://purl.obolibrary.org/obo/RO_0010001> is carrier of > <http://purl.obolibrary.org/obo/RO_0010002> ) > - is carrier of <http://purl.obolibrary.org/obo/RO_0010002> *definition > <http://purl.obolibrary.org/obo/IAO_0000115>* *b* is carrier of *c* at > time *t* if and only if *c* *g-depends on* *b* at *t* > - is carrier of <http://purl.obolibrary.org/obo/RO_0010002> *example > of usage <http://purl.obolibrary.org/obo/IAO_0000112>* This copy of *War > and Peace* is carrier of the novel written by Tolstoy. > - ObjectPropertyRange( is carrier of > <http://purl.obolibrary.org/obo/RO_0010002> generically dependent > continuant <http://purl.obolibrary.org/obo/BFO_0000031> ) > - is carrier of <http://purl.obolibrary.org/obo/RO_0010002> *example > of usage <http://purl.obolibrary.org/obo/IAO_0000112>* Molecules of > DNA are carriers of genetic information. > > Changed ObjectProperty objects: 58 Changes for: in taxon > <http://purl.obolibrary.org/obo/RO_0002162> > > - *Deleted* > - *-* ObjectPropertyRange( in taxon > <http://purl.obolibrary.org/obo/RO_0002162> independent continuant > <http://purl.obolibrary.org/obo/BFO_0000004> ) > - *Added* > - *+* ObjectPropertyRange( in taxon > <http://purl.obolibrary.org/obo/RO_0002162> organism or virus or > viroid <http://purl.obolibrary.org/obo/CARO_0001010> ) > > Changes for: results in maturation of > <http://purl.obolibrary.org/obo/RO_0002299> > > - *Deleted* > - *-* SubObjectPropertyOf( results in maturation of > <http://purl.obolibrary.org/obo/RO_0002299> has participant > <http://purl.obolibrary.org/obo/RO_0000057> ) > - *Added* > - *+* SubObjectPropertyOf( results in maturation of > <http://purl.obolibrary.org/obo/RO_0002299> has anatomical > participant <http://purl.obolibrary.org/obo/RO_0040036> ) > > Changes for: attached to part of > <http://purl.obolibrary.org/obo/RO_0002177> > > - *Deleted* > - *-* ObjectPropertyDomain( attached to part of > <http://purl.obolibrary.org/obo/RO_0002177> material entity > <http://purl.obolibrary.org/obo/BFO_0000040> ) > - *-* ObjectPropertyRange( attached to part of > <http://purl.obolibrary.org/obo/RO_0002177> material entity > <http://purl.obolibrary.org/obo/BFO_0000040> ) > - *Added* > - *+* ObjectPropertyDomain( attached to part of > <http://purl.obolibrary.org/obo/RO_0002177> anatomical structure > <http://purl.obolibrary.org/obo/CARO_0000003> ) > - *+* ObjectPropertyRange( attached to part of > <http://purl.obolibrary.org/obo/RO_0002177> anatomical structure > <http://purl.obolibrary.org/obo/CARO_0000003> ) > - *+* attached to part of > <http://purl.obolibrary.org/obo/RO_0002177> *OBO foundry unique > label <http://purl.obolibrary.org/obo/IAO_0000589>* attached to > part of (anatomical structure to anatomical structure) > > Changes for: results in morphogenesis of > <http://purl.obolibrary.org/obo/RO_0002298> > > - *Deleted* > - *-* SubObjectPropertyOf( results in morphogenesis of > <http://purl.obolibrary.org/obo/RO_0002298> has participant > <http://purl.obolibrary.org/obo/RO_0000057> ) > - *Added* > - *+* SubObjectPropertyOf( results in morphogenesis of > <http://purl.obolibrary.org/obo/RO_0002298> has anatomical > participant <http://purl.obolibrary.org/obo/RO_0040036> ) > > Changes for: results in development of > <http://purl.obolibrary.org/obo/RO_0002296> > > - *Deleted* > - *-* SubObjectPropertyOf( results in development of > <http://purl.obolibrary.org/obo/RO_0002296> has participant > <http://purl.obolibrary.org/obo/RO_0000057> ) > - *Added* > - *+* SubObjectPropertyOf( results in development of > <http://purl.obolibrary.org/obo/RO_0002296> has anatomical > participant <http://purl.obolibrary.org/obo/RO_0040036> ) > > Changes for: disease has inflammation site > <http://purl.obolibrary.org/obo/RO_0004027> > > - *Added* > - *+* ObjectPropertyDomain( disease has inflammation site > <http://purl.obolibrary.org/obo/RO_0004027> disease > <http://purl.obolibrary.org/obo/OGMS_0000031> ) > - *+* ObjectPropertyRange( disease has inflammation site > <http://purl.obolibrary.org/obo/RO_0004027> anatomical structure > <http://purl.obolibrary.org/obo/CARO_0000003> ) > > Changes for: creates habitat for > <http://purl.obolibrary.org/obo/RO_0008505> > > - *Added* > - *+* ObjectPropertyDomain( creates habitat for > <http://purl.obolibrary.org/obo/RO_0008505> organism or virus or > viroid <http://purl.obolibrary.org/obo/CARO_0001010> ) > - *+* ObjectPropertyRange( creates habitat for > <http://purl.obolibrary.org/obo/RO_0008505> organism or virus or > viroid <http://purl.obolibrary.org/obo/CARO_0001010> ) > > Changes for: disease has feature > <http://purl.obolibrary.org/obo/RO_0004029> > > - *Deleted* > - *-* ObjectPropertyRange( disease has feature > <http://purl.obolibrary.org/obo/RO_0004029> disposition > <http://purl.obolibrary.org/obo/BFO_0000016> *or* quality > <http://purl.obolibrary.org/obo/BFO_0000019> ) > - *-* SubObjectPropertyOf( disease has feature > <http://purl.obolibrary.org/obo/RO_0004029> causal relationship > with disease as subject <http://purl.obolibrary.org/obo/RO_0004023> > ) > - *Added* > - *+* ObjectPropertyDomain( disease has feature > <http://purl.obolibrary.org/obo/RO_0004029> disease > <http://purl.obolibrary.org/obo/OGMS_0000031> ) > - *+* ObjectPropertyRange( disease has feature > <http://purl.obolibrary.org/obo/RO_0004029> disease > <http://purl.obolibrary.org/obo/OGMS_0000031> *or* phenotype > <http://purl.obolibrary.org/obo/UPHENO_0001001> ) > - *+* SubObjectPropertyOf( disease has feature > <http://purl.obolibrary.org/obo/RO_0004029> disease relationship > <http://purl.obolibrary.org/obo/RO_0040035> ) > > Changes for: ecologically co-occurs with > <http://purl.obolibrary.org/obo/RO_0008506> > > - *Deleted* > - *-* co-occurs <http://purl.obolibrary.org/obo/RO_0008506> *label > <http://www.w3.org/2000/01/rdf-schema#label>* co-occurs > - *Added* > - *+* ObjectPropertyDomain( ecologically co-occurs with > <http://purl.obolibrary.org/obo/RO_0008506> organism or virus or > viroid <http://purl.obolibrary.org/obo/CARO_0001010> ) > - *+* ObjectPropertyRange( ecologically co-occurs with > <http://purl.obolibrary.org/obo/RO_0008506> organism or virus or > viroid <http://purl.obolibrary.org/obo/CARO_0001010> ) > - *+* ecologically co-occurs with > <http://purl.obolibrary.org/obo/RO_0008506> *label > <http://www.w3.org/2000/01/rdf-schema#label>* ecologically > co-occurs with > > Changes for: disease has basis in dysfunction of > <http://purl.obolibrary.org/obo/RO_0004020> > > - *Deleted* > - *-* ObjectPropertyRange( disease has basis in dysfunction of > <http://purl.obolibrary.org/obo/RO_0004020> material entity > <http://purl.obolibrary.org/obo/BFO_0000040> ) > - *Added* > - *+* ObjectPropertyRange( disease has basis in dysfunction of > <http://purl.obolibrary.org/obo/RO_0004020> material anatomical > entity <http://purl.obolibrary.org/obo/CARO_0000006> ) > - *+* disease has basis in dysfunction of > <http://purl.obolibrary.org/obo/RO_0004020> *OBO foundry unique > label <http://purl.obolibrary.org/obo/IAO_0000589>* disease has > basis in dysfunction of (disease to anatomical structure) > > Changes for: disease has basis in disruption of > <http://purl.obolibrary.org/obo/RO_0004021> > > - *Added* > - *+* disease has basis in disruption of > <http://purl.obolibrary.org/obo/RO_0004021> *OBO foundry unique > label <http://purl.obolibrary.org/obo/IAO_0000589>* disease has > basis in disruption of (disease to process) > > Changes for: disease has basis in feature > <http://purl.obolibrary.org/obo/RO_0004022> > > - *Added* > - *+* ObjectPropertyDomain( disease has basis in feature > <http://purl.obolibrary.org/obo/RO_0004022> disease > <http://purl.obolibrary.org/obo/OGMS_0000031> ) > - *+* ObjectPropertyRange( disease has basis in feature > <http://purl.obolibrary.org/obo/RO_0004022> disease > <http://purl.obolibrary.org/obo/OGMS_0000031> *or* phenotype > <http://purl.obolibrary.org/obo/UPHENO_0001001> ) > > Changes for: causal relationship with disease as subject > <http://purl.obolibrary.org/obo/RO_0004023> > > - *Deleted* > - *-* ObjectPropertyDomain( causal relationship with disease as > subject <http://purl.obolibrary.org/obo/RO_0004023> disposition > <http://purl.obolibrary.org/obo/BFO_0000016> ) > - *Added* > - *+* ObjectPropertyDomain( causal relationship with disease as > subject <http://purl.obolibrary.org/obo/RO_0004023> disease > <http://purl.obolibrary.org/obo/OGMS_0000031> ) > - *+* SubObjectPropertyOf( causal relationship with disease as > subject <http://purl.obolibrary.org/obo/RO_0004023> disease > relationship <http://purl.obolibrary.org/obo/RO_0040035> ) > > Changes for: disease causes disruption of > <http://purl.obolibrary.org/obo/RO_0004024> > > - *Added* > - *+* ObjectPropertyDomain( disease causes disruption of > <http://purl.obolibrary.org/obo/RO_0004024> disease > <http://purl.obolibrary.org/obo/OGMS_0000031> ) > - *+* disease causes disruption of > <http://purl.obolibrary.org/obo/RO_0004024> *OBO foundry unique > label <http://purl.obolibrary.org/obo/IAO_0000589>* disease causes > disruption of (disease to process) > > Changes for: disease causes dysfunction of > <http://purl.obolibrary.org/obo/RO_0004025> > > - *Deleted* > - *-* ObjectPropertyRange( disease causes dysfunction of > <http://purl.obolibrary.org/obo/RO_0004025> independent continuant > <http://purl.obolibrary.org/obo/BFO_0000004> ) > - *Added* > - *+* ObjectPropertyDomain( disease causes dysfunction of > <http://purl.obolibrary.org/obo/RO_0004025> disease > <http://purl.obolibrary.org/obo/OGMS_0000031> ) > - *+* ObjectPropertyRange( disease causes dysfunction of > <http://purl.obolibrary.org/obo/RO_0004025> material anatomical > entity <http://purl.obolibrary.org/obo/CARO_0000006> ) > - *+* disease causes dysfunction of > <http://purl.obolibrary.org/obo/RO_0004025> *OBO foundry unique > label <http://purl.obolibrary.org/obo/IAO_0000589>* disease causes > dysfunction of (disease to anatomical entity) > > Changes for: disease has location > <http://purl.obolibrary.org/obo/RO_0004026> > > - *Deleted* > - *-* SubObjectPropertyOf( disease has location > <http://purl.obolibrary.org/obo/RO_0004026> causal relationship > with disease as subject <http://purl.obolibrary.org/obo/RO_0004023> > ) > - *Added* > - *+* ObjectPropertyDomain( disease has location > <http://purl.obolibrary.org/obo/RO_0004026> disease > <http://purl.obolibrary.org/obo/OGMS_0000031> ) > - *+* ObjectPropertyRange( disease has location > <http://purl.obolibrary.org/obo/RO_0004026> material anatomical > entity <http://purl.obolibrary.org/obo/CARO_0000006> *or* immaterial > anatomical entity <http://purl.obolibrary.org/obo/CARO_0000007> ) > - *+* SubObjectPropertyOf( disease has location > <http://purl.obolibrary.org/obo/RO_0004026> disease relationship > <http://purl.obolibrary.org/obo/RO_0040035> ) > > Changes for: disease has basis in > <http://purl.obolibrary.org/obo/RO_0004019> > > - *Deleted* > - *-* ObjectPropertyDomain( disease has basis in > <http://purl.obolibrary.org/obo/RO_0004019> disposition > <http://purl.obolibrary.org/obo/BFO_0000016> ) > - *Added* > - *+* ObjectPropertyDomain( disease has basis in > <http://purl.obolibrary.org/obo/RO_0004019> disease > <http://purl.obolibrary.org/obo/OGMS_0000031> ) > > Changes for: has phenotype <http://purl.obolibrary.org/obo/RO_0002200> > > - *Deleted* > - *-* ObjectPropertyDomain( has phenotype > <http://purl.obolibrary.org/obo/RO_0002200> continuant > <http://purl.obolibrary.org/obo/BFO_0000002> ) > - *Added* > - *+* ObjectPropertyDomain( has phenotype > <http://purl.obolibrary.org/obo/RO_0002200> generically dependent > continuant <http://purl.obolibrary.org/obo/BFO_0000031> *or* material > anatomical entity <http://purl.obolibrary.org/obo/CARO_0000006> *or* > disease <http://purl.obolibrary.org/obo/OGMS_0000031> ) > - *+* ObjectPropertyRange( has phenotype > <http://purl.obolibrary.org/obo/RO_0002200> phenotype > <http://purl.obolibrary.org/obo/UPHENO_0001001> ) > > Changes for: ecologically related to > <http://purl.obolibrary.org/obo/RO_0002321> > > - *Added* > - *+* ecologically related to > <http://purl.obolibrary.org/obo/RO_0002321> *editor note > <http://purl.obolibrary.org/obo/IAO_0000116>* Awaiting class for > domain/range constraint, see: > https://github.com/OBOFoundry/Experimental-OBO-Core/issues/6 > > Changes for: functionally related to > <http://purl.obolibrary.org/obo/RO_0002328> > > - *Added* > - *+* functionally related to > <http://purl.obolibrary.org/obo/RO_0002328> *definition > <http://purl.obolibrary.org/obo/IAO_0000115>* A grouping > relationship for any relationship directly involving a function, or that > holds because of a function of one of the related entities. > > Changes for: expressed in <http://purl.obolibrary.org/obo/RO_0002206> > > - *Deleted* > - *-* ObjectPropertyRange( expressed in > <http://purl.obolibrary.org/obo/RO_0002206> independent continuant > <http://purl.obolibrary.org/obo/BFO_0000004> ) > - *Added* > - *+* ObjectPropertyRange( expressed in > <http://purl.obolibrary.org/obo/RO_0002206> material anatomical > entity <http://purl.obolibrary.org/obo/CARO_0000006> ) > > Changes for: biomechanically related to > <http://purl.obolibrary.org/obo/RO_0002567> > > - *Added* > - *+* ObjectPropertyDomain( biomechanically related to > <http://purl.obolibrary.org/obo/RO_0002567> anatomical structure > <http://purl.obolibrary.org/obo/CARO_0000003> ) > - *+* ObjectPropertyRange( biomechanically related to > <http://purl.obolibrary.org/obo/RO_0002567> anatomical structure > <http://purl.obolibrary.org/obo/CARO_0000003> ) > > Changes for: results in movement of > <http://purl.obolibrary.org/obo/RO_0002565> > > - *Deleted* > - *-* SubObjectPropertyOf( results in movement of > <http://purl.obolibrary.org/obo/RO_0002565> has participant > <http://purl.obolibrary.org/obo/RO_0000057> ) > - *Added* > - *+* SubObjectPropertyOf( results in movement of > <http://purl.obolibrary.org/obo/RO_0002565> has anatomical > participant <http://purl.obolibrary.org/obo/RO_0040036> ) > > Changes for: confers advantage in > <http://purl.obolibrary.org/obo/RO_0002322> > > - *Added* > - *+* ObjectPropertyRange( confers advantage in > <http://purl.obolibrary.org/obo/RO_0002322> environmental system > <http://purl.obolibrary.org/obo/ENVO_01000254> ) > > Changes for: involved in or involved in regulation of > <http://purl.obolibrary.org/obo/RO_0002431> > > - *Added* > - *+* involved in or involved in regulation of > <http://purl.obolibrary.org/obo/RO_0002431> *editor note > <http://purl.obolibrary.org/obo/IAO_0000116>* OWL does not allow > defining object properties via a Union > > Changes for: results in ending of > <http://purl.obolibrary.org/obo/RO_0002552> > > - *Deleted* > - *-* SubObjectPropertyOf( results in ending of > <http://purl.obolibrary.org/obo/RO_0002552> has participant > <http://purl.obolibrary.org/obo/RO_0000057> ) > - *Added* > - *+* SubObjectPropertyOf( results in ending of > <http://purl.obolibrary.org/obo/RO_0002552> has anatomical > participant <http://purl.obolibrary.org/obo/RO_0040036> ) > > Changes for: results in acquisition of features of > <http://purl.obolibrary.org/obo/RO_0002315> > > - *Deleted* > - *-* ObjectPropertyRange( results in acquisition of features of > <http://purl.obolibrary.org/obo/RO_0002315> cell > <http://purl.obolibrary.org/obo/CL_0000000> ) > - *-* SubObjectPropertyOf( results in acquisition of features of > <http://purl.obolibrary.org/obo/RO_0002315> has participant > <http://purl.obolibrary.org/obo/RO_0000057> ) > - *Added* > - *+* ObjectPropertyRange( results in acquisition of features of > <http://purl.obolibrary.org/obo/RO_0002315> anatomical structure > <http://purl.obolibrary.org/obo/CARO_0000003> ) > - *+* SubObjectPropertyOf( results in acquisition of features of > <http://purl.obolibrary.org/obo/RO_0002315> has anatomical > participant <http://purl.obolibrary.org/obo/RO_0040036> ) > > Changes for: inheres in part of > <http://purl.obolibrary.org/obo/RO_0002314> > > - *Added* > - *+* inheres in part of <http://purl.obolibrary.org/obo/RO_0002314> *seeAlso > <http://www.w3.org/2000/01/rdf-schema#seeAlso>* > defining-property-chains-involving-reflexivity > <https://github.com/oborel/obo-relations/wiki/ROGuide#defining-property-chains-involving-reflexivity> > > Changes for: transports or maintains localization of > <http://purl.obolibrary.org/obo/RO_0002313> > > - *Deleted* > - *-* SubObjectPropertyOf( transports or maintains localization of > <http://purl.obolibrary.org/obo/RO_0002313> has participant > <http://purl.obolibrary.org/obo/RO_0000057> ) > - *Added* > - *+* SubObjectPropertyOf( transports or maintains localization of > <http://purl.obolibrary.org/obo/RO_0002313> has anatomical > participant <http://purl.obolibrary.org/obo/RO_0040036> ) > > Changes for: results in growth of > <http://purl.obolibrary.org/obo/RO_0002343> > > - *Deleted* > - *-* SubObjectPropertyOf( results in growth of > <http://purl.obolibrary.org/obo/RO_0002343> has participant > <http://purl.obolibrary.org/obo/RO_0000057> ) > - *Added* > - *+* SubObjectPropertyOf( results in growth of > <http://purl.obolibrary.org/obo/RO_0002343> has anatomical > participant <http://purl.obolibrary.org/obo/RO_0040036> ) > > Changes for: helper property (not for use in curation) > <http://purl.obolibrary.org/obo/RO_0002464> > > - *Deleted* > - *-* helper property <http://purl.obolibrary.org/obo/RO_0002464> *label > <http://www.w3.org/2000/01/rdf-schema#label>* helper property > - *Added* > - *+* helper property (not for use in curation) > <http://purl.obolibrary.org/obo/RO_0002464> *label > <http://www.w3.org/2000/01/rdf-schema#label>* helper property (not > for use in curation) > > Changes for: results in closure of > <http://purl.obolibrary.org/obo/RO_0002585> > > - *Deleted* > - *-* SubObjectPropertyOf( results in closure of > <http://purl.obolibrary.org/obo/RO_0002585> has participant > <http://purl.obolibrary.org/obo/RO_0000057> ) > - *Added* > - *+* SubObjectPropertyOf( results in closure of > <http://purl.obolibrary.org/obo/RO_0002585> has anatomical > participant <http://purl.obolibrary.org/obo/RO_0040036> ) > > Changes for: has soma location <http://purl.obolibrary.org/obo/RO_0002100> > > - *Added* > - *+* ObjectPropertyRange( has soma location > <http://purl.obolibrary.org/obo/RO_0002100> anatomical structure > <http://purl.obolibrary.org/obo/CARO_0000003> ) > > Changes for: participates in a biotic-biotic interaction with > <http://purl.obolibrary.org/obo/RO_0002574> > > - *Added* > - *+* ObjectPropertyDomain( participates in a biotic-biotic > interaction with <http://purl.obolibrary.org/obo/RO_0002574> organism > or virus or viroid <http://purl.obolibrary.org/obo/CARO_0001010> ) > - *+* ObjectPropertyRange( participates in a biotic-biotic > interaction with <http://purl.obolibrary.org/obo/RO_0002574> organism > or virus or viroid <http://purl.obolibrary.org/obo/CARO_0001010> ) > > Changes for: has modifier <http://purl.obolibrary.org/obo/RO_0002573> > > - *Added* > - *+* ObjectPropertyRange( has modifier > <http://purl.obolibrary.org/obo/RO_0002573> specifically dependent > continuant <http://purl.obolibrary.org/obo/BFO_0000020> ) > > Changes for: capable of part of > <http://purl.obolibrary.org/obo/RO_0002216> > > - *Added* > - *+* capable of part of <http://purl.obolibrary.org/obo/RO_0002216> *seeAlso > <http://www.w3.org/2000/01/rdf-schema#seeAlso>* > defining-property-chains-involving-reflexivity > <https://github.com/oborel/obo-relations/wiki/ROGuide#defining-property-chains-involving-reflexivity> > > Changes for: has prototype <http://purl.obolibrary.org/obo/RO_0002214> > > - *Added* > - *+* ObjectPropertyDomain( has prototype > <http://purl.obolibrary.org/obo/RO_0002214> independent continuant > <http://purl.obolibrary.org/obo/BFO_0000004> *or* process > <http://purl.obolibrary.org/obo/BFO_0000015> ) > > Changes for: enabled by <http://purl.obolibrary.org/obo/RO_0002333> > > - *Deleted* > - *-* SubObjectPropertyOf( enabled by > <http://purl.obolibrary.org/obo/RO_0002333> undefined( ) ) > > Changes for: aligned with <http://purl.obolibrary.org/obo/RO_0002001> > > - *Added* > - *+* aligned with <http://purl.obolibrary.org/obo/RO_0002001> *editor > note <http://purl.obolibrary.org/obo/IAO_0000116>* May be > obsoleted, see https://github.com/oborel/obo-relations/issues/260 > > Changes for: innervated_by <http://purl.obolibrary.org/obo/RO_0002005> > > - *Added* > - *+* ObjectPropertyDomain( innervated by > <http://purl.obolibrary.org/obo/RO_0002005> anatomical structure > <http://purl.obolibrary.org/obo/CARO_0000003> ) > - *+* ObjectPropertyRange( innervated by > <http://purl.obolibrary.org/obo/RO_0002005> neuron projection bundle > <http://purl.obolibrary.org/obo/CARO_0001001> ) > > Changes for: tracheates <http://purl.obolibrary.org/obo/RO_0002004> > > - *Added* > - *+* ObjectPropertyDomain( tracheates > <http://purl.obolibrary.org/obo/RO_0002004> anatomical structure > <http://purl.obolibrary.org/obo/CARO_0000003> ) > - *+* ObjectPropertyRange( tracheates > <http://purl.obolibrary.org/obo/RO_0002004> anatomical structure > <http://purl.obolibrary.org/obo/CARO_0000003> ) > > Changes for: relation between structure and stage > <http://purl.obolibrary.org/obo/RO_0002487> > > - *Added* > - *+* ObjectPropertyDomain( relation between structure and stage > <http://purl.obolibrary.org/obo/RO_0002487> material anatomical > entity <http://purl.obolibrary.org/obo/CARO_0000006> *or* immaterial > anatomical entity <http://purl.obolibrary.org/obo/CARO_0000007> ) > > Changes for: releases neurotransmitter > <http://purl.obolibrary.org/obo/RO_0002111> > > - *Added* > - *+* ObjectPropertyDomain( releases neurotransmitter > <http://purl.obolibrary.org/obo/RO_0002111> anatomical structure > <http://purl.obolibrary.org/obo/CARO_0000003> ) > > Changes for: results in organization of > <http://purl.obolibrary.org/obo/RO_0002592> > > - *Deleted* > - *-* SubObjectPropertyOf( results in organization of > <http://purl.obolibrary.org/obo/RO_0002592> has participant > <http://purl.obolibrary.org/obo/RO_0000057> ) > - *Added* > - *+* SubObjectPropertyOf( results in organization of > <http://purl.obolibrary.org/obo/RO_0002592> has anatomical > participant <http://purl.obolibrary.org/obo/RO_0040036> ) > > Changes for: results in structural organization of > <http://purl.obolibrary.org/obo/RO_0002355> > > - *Deleted* > - *-* SubObjectPropertyOf( results in structural organization of > <http://purl.obolibrary.org/obo/RO_0002355> has participant > <http://purl.obolibrary.org/obo/RO_0000057> ) > - *Added* > - *+* SubObjectPropertyOf( results in structural organization of > <http://purl.obolibrary.org/obo/RO_0002355> has anatomical > participant <http://purl.obolibrary.org/obo/RO_0040036> ) > > Changes for: derived from ancestral fusion of > <http://purl.obolibrary.org/obo/RO_0002374> > > - *Deleted* > - *-* SubObjectPropertyOf( has fused element > <http://purl.obolibrary.org/obo/RO_0002374> evolutionarily related > to <http://purl.obolibrary.org/obo/RO_0002320> ) > - *-* has fused element <http://purl.obolibrary.org/obo/RO_0002374> *label > <http://www.w3.org/2000/01/rdf-schema#label>* has fused element > - *Added* > - *+* SubObjectPropertyOf( derived from ancestral fusion of > <http://purl.obolibrary.org/obo/RO_0002374> derived by descent from > <http://purl.obolibrary.org/obo/RO_0002156> ) > - *+* derived from ancestral fusion of > <http://purl.obolibrary.org/obo/RO_0002374> *has broad synonym > <http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym>* has > fused element > - *+* derived from ancestral fusion of > <http://purl.obolibrary.org/obo/RO_0002374> *label > <http://www.w3.org/2000/01/rdf-schema#label>* derived from > ancestral fusion of > > Changes for: has muscle insertion > <http://purl.obolibrary.org/obo/RO_0002373> > > - *Added* > - *+* ObjectPropertyDomain( has muscle insertion > <http://purl.obolibrary.org/obo/RO_0002373> anatomical structure > <http://purl.obolibrary.org/obo/CARO_0000003> ) { editor note > <http://purl.obolibrary.org/obo/IAO_0000116>=We need to import > uberon muscle into RO to use as a stricter domain constraint } > > Changes for: has muscle origin <http://purl.obolibrary.org/obo/RO_0002372> > > - *Added* > - *+* ObjectPropertyDomain( has muscle origin > <http://purl.obolibrary.org/obo/RO_0002372> anatomical structure > <http://purl.obolibrary.org/obo/CARO_0000003> ) { comment > <http://www.w3.org/2000/01/rdf-schema#comment>=We need to import > uberon muscle to create a stricter domain constraint } > > Changes for: attached to <http://purl.obolibrary.org/obo/RO_0002371> > > - *Added* > - *+* attached to <http://purl.obolibrary.org/obo/RO_0002371> *OBO > foundry unique label <http://purl.obolibrary.org/obo/IAO_0000589>* > attached to (anatomical structure to anatomical structure) > > Changes for: in neural circuit with > <http://purl.obolibrary.org/obo/RO_0000300> > > - *Added* > - *+* ObjectPropertyDomain( in neural circuit with > <http://purl.obolibrary.org/obo/RO_0000300> neuron > <http://purl.obolibrary.org/obo/CL_0000540> ) > - *+* ObjectPropertyRange( in neural circuit with > <http://purl.obolibrary.org/obo/RO_0000300> neuron > <http://purl.obolibrary.org/obo/CL_0000540> ) > > Changes for: obsolete related via dependence to > <http://purl.obolibrary.org/obo/RO_0002609> > > - *Deleted* > - *-* related via dependence to > <http://purl.obolibrary.org/obo/RO_0002609> *label > <http://www.w3.org/2000/01/rdf-schema#label>* related via > dependence to > - *Added* > - *+* obsolete related via dependence to > <http://purl.obolibrary.org/obo/RO_0002609> *deprecated > <http://www.w3.org/2002/07/owl#deprecated>* true > - *+* obsolete related via dependence to > <http://purl.obolibrary.org/obo/RO_0002609> *label > <http://www.w3.org/2000/01/rdf-schema#label>* obsolete related via > dependence to > > Changes for: has substance added > <http://purl.obolibrary.org/obo/RO_0009001> > > - *Added* > - *+* ObjectPropertyDomain( has substance added > <http://purl.obolibrary.org/obo/RO_0009001> material entity > <http://purl.obolibrary.org/obo/BFO_0000040> ) > - *+* ObjectPropertyRange( has substance added > <http://purl.obolibrary.org/obo/RO_0009001> material entity > <http://purl.obolibrary.org/obo/BFO_0000040> ) > > Changes for: has substance removed > <http://purl.obolibrary.org/obo/RO_0009002> > > - *Added* > - *+* ObjectPropertyDomain( has substance removed > <http://purl.obolibrary.org/obo/RO_0009002> material entity > <http://purl.obolibrary.org/obo/BFO_0000040> ) > - *+* ObjectPropertyRange( has substance removed > <http://purl.obolibrary.org/obo/RO_0009002> material entity > <http://purl.obolibrary.org/obo/BFO_0000040> ) > > Changes for: immersed in <http://purl.obolibrary.org/obo/RO_0009003> > > - *Added* > - *+* ObjectPropertyDomain( immersed in > <http://purl.obolibrary.org/obo/RO_0009003> material entity > <http://purl.obolibrary.org/obo/BFO_0000040> ) > - *+* ObjectPropertyRange( immersed in > <http://purl.obolibrary.org/obo/RO_0009003> material entity > <http://purl.obolibrary.org/obo/BFO_0000040> ) > > Changes for: correlated with <http://purl.obolibrary.org/obo/RO_0002610> > > - *Deleted* > - *-* SubObjectPropertyOf( correlated with > <http://purl.obolibrary.org/obo/RO_0002610> related via dependence > to <http://purl.obolibrary.org/obo/RO_0002609> ) > > Changes for: obsolete has indirect output > <http://purl.obolibrary.org/obo/RO_0002403> > > - *Deleted* > - *-* SubObjectPropertyOf( obsolete has indirect output > <http://purl.obolibrary.org/obo/RO_0002403> has output > <http://purl.obolibrary.org/obo/RO_0002234> ) > > Changes for: has habitat <http://purl.obolibrary.org/obo/RO_0002303> > > - *Deleted* > - *-* ObjectPropertyDomain( has habitat > <http://purl.obolibrary.org/obo/RO_0002303> material anatomical > entity <http://purl.obolibrary.org/obo/CARO_0000006> ) > - *Added* > - *+* ObjectPropertyDomain( has habitat > <http://purl.obolibrary.org/obo/RO_0002303> organism or virus or > viroid <http://purl.obolibrary.org/obo/CARO_0001010> ) > > Changes for: causally related to > <http://purl.obolibrary.org/obo/RO_0002410> > > - *Deleted* > - *-* SubObjectPropertyOf( causally related to > <http://purl.obolibrary.org/obo/RO_0002410> related via dependence > to <http://purl.obolibrary.org/obo/RO_0002609> ) > > |
From: hunteronsabbatical <hun...@gm...> - 2018-08-28 15:43:44
|
Is it the same as last time? That is, Description:https://arizona.zoom.us/j/342742288 Topic: OBO Foundry Operations Committee Time: This is a recurring meeting. Meet anytime. Join from PC, Mac, Linux, iOS or Android: https://arizona.zoom.us/j/342742288 Or iPhone one-tap : US: +16468769923,,342742288# or +16699006833,,342742288# Or Telephone: Dial(for higher quality, dial a number based on your current location): US: +1 646 876 9923 or +1 669 900 6833 Meeting ID: 342 742 288 International numbers available: https://zoom.us/u/o7wsHwT8 Or an H.323/SIP room system: H.323: 162.255.37.11 (US West) 162.255.36.11 (US East) 221.122.88.195 (China) 115.114.131.7 (India) 213.19.144.110 (EMEA) 202.177.207.158 (Australia) 209.9.211.110 (Hong Kong) 64.211.144.160 (Brazil) 69.174.57.160 (Canada) Meeting ID: 342 742 288 |
From: Barry S. <if...@gm...> - 2018-08-28 15:40:02
|
Slides for today's call are attached BS |
From: hunteronsabbatical <hun...@gm...> - 2018-08-28 15:25:39
|
Are the call-in details the same as Aug 13? I.e. Description:https://arizona.zoom.us/j/342742288 ------------------------------ Topic: OBO Foundry Operations Committee Time: This is a recurring meeting. Meet anytime. Join from PC, Mac, Linux, iOS or Android: https://arizona.zoom.us/j/342742288 Or iPhone one-tap : US: +16468769923,,342742288# or +16699006833,,342742288# Or Telephone: Dial(for higher quality, dial a number based on your current location): US: +1 646 876 9923 or +1 669 900 6833 Meeting ID: 342 742 288 International numbers available: https://zoom.us/u/o7wsHwT8 Or an H.323/SIP room system: H.323: 162.255.37.11 (US West) 162.255.36.11 (US East) 221.122.88.195 (China) 115.114.131.7 (India) 213.19.144.110 (EMEA) 202.177.207.158 (Australia) 209.9.211.110 (Hong Kong) 64.211.144.160 (Brazil) 69.174.57.160 (Canada) Meeting ID: 342 742 288 SIP: 3427...@zoomcrc.com |
From: Barry S. <if...@gm...> - 2018-08-28 14:19:50
|
Ideas for Agenda: 1. BFO-ISO General outline of current state, with implications for RO 2. Transitivity of 'part-of' 3. RO, RO-CORE, RO-Extended-CORE Further suggestions welcome. Re Item 1: BS will provide slides in advance of the meeting Re Item 2: A topic discussed at the ICBO meeting was the transitivity of part-of, and possible failures thereof as a result of the fact that one entity may be part of a second entity only for a certain part of the history of that second entity. An example of such failure proposed by Alan Ruttenberg is: phagosome part of macrophage macrophage part of bone marrow but not: phagosome part of bone marrow Another example (not from Alan) is: 11th Hussars (Prince Albert's Own) part of King's Royal Hussars King's Royal Hussars part of 12th Armoured Infantry Brigade but not 11th Hussars (Prince Albert's Own)part of 12th Armoured Infantry Brigade This is because the 11th Hussars (Prince Albert's Own) were disbanded before the 12th Armoured Infantry Brigade was formed. Although such examples are rare, there are areas (especially development) where the logic of part-of will need to be carefully tailored to fit. Note that such examples only arise in the realm of continuants. Part of is trivially transitive for occurrents, since occurrents do not gain and lose parts. Re Item 3: Another RO topic discussed at the ICBO meeting we discussed the idea of extending RO-CORE by adding a collection of further general relations -- such as input, output, about -- which should be recommended for use by all RO users, but which are not part of RO Core since they are not part of the scope of BFO. In this connection it was pointed out that the Common Core Ontologies (CCO) -- see ( https://www.cubrc.org/index.php/data-science-and-information-fusion/ontology) -- have already created such a set of general-purpose relations, which are available (https://buffalo.box.com/s/fte3zj3i86ni6u9npt2brvy1dg4kvwbo) They are divided into 6 groups, first is the CCO equivalent of our RO Core, followed by: Agent Ontology Geospatial Ontology Information Entity Ontology Time Ontology Extended Relation Ontology (mainly for relations pointing to entities in the future) People are invited to examine these relations and identify those which they think will be of value for OBO purposes. |
From: Barry S. <phi...@bu...> - 2018-08-27 21:49:13
|
1. RO, RO-CORE, RO-Extended-CORE 2. BFO-ISO General outline of current state, with implications for RO Further suggestions welcome. BS |
From: Barry S. <phi...@bu...> - 2018-08-27 15:29:15
|
Another topic discussed at the ICBO meeting was the transitivity of part-of, and possible failures thereof as a result of the fact that one entity may be part of a second entity only for a certain part of the history of that second entity. An example of such failure proposed by Alan Ruttenberg is: phagosome part of macrophage macrophage part of bone marrow but not: phagosome part of bone marrow Another example (not from Alan) is: 11th Hussars (Prince Albert's Own) part of King's Royal Hussars King's Royal Hussars part of 12th Armoured Infantry Brigade but not 11th Hussars (Prince Albert's Own) part of 12th Armoured Infantry Brigade This is because the King's Royal Hussars were disbanded before the 12th Armoured Infantry Brigade was formed. Although such examples are rare, there are areas (especially development) where the logic of part-of will need to be carefully tailored to fit. Note that such examples only arise in the realm of continuants. Part of is trivially transitive for occurrents, since occurrents do not gain and lose parts. BS |
From: Barry S. <phi...@bu...> - 2018-08-27 15:27:44
|
In the RO discussion at the ICBO meeting we discussed the idea of extending RO-CORE by adding a collection of further general relations -- such as input, output, about -- which should be recommended for use by all RO users, but which are not part of RO Core since they are not part of the scope of BFO. In this connection it was pointed out that the Common Core Ontologies (CCO) -- see ( https://www.cubrc.org/index.php/data-science-and-information-fusion/ontology) -- have already created such a set of general-purpose relations, which are available (https://buffalo.box.com/s/fte3zj3i86ni6u9npt2brvy1dg4kvwbo) They are divided into groups, first is the CCO equivalent of our RO Core, followed by: Agent Ontology Geospatial Ontology Information Entity Ontology Time Ontology Extended Relation Ontology (mainly for relations pointing to entities in the future) People are invited to examine these relations and identify those which they think will be of value for general OBO purposes. BS |