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Request for new ontology - Experimental Measurements, Purposes, and Treatments ontology

Open andreagaede opened this issue 8 months ago • 29 comments

Title

Experimental Measurements, Purposes, and Treatments ontologY

Short Description

An ontology of experimental measurements in the sciences, the purposes for which experimental measurements were made, and experimental treatments, with a focus on life sciences.

Description

The Experimental Measurements, Purposes, and Treatments ontologY (EMPTY) is a structured vocabulary designed to capture and standardize the scientific reasoning behind experimental measurements. It addresses a critical gap in existing metadata standards, which primarily focus on technical specifications rather than scientific intent. The ontology provides a common language to express why a measurement was taken and the conceptual conditions under which it should be interpreted. By focusing on experimental purposes and treatments, EMPTY is designed to significantly improve the findability, interoperability, and reusability of scientific data. This enables researchers to discover relevant datasets for meta-analyses and cross-disciplinary research based on shared scientific goals.

Identifier Space

EMPTY

License

CC-BY 4.0

Domain

investigations

Source Code Repository

https://github.com/Waltham-Data-Science/empty-ontology

Homepage

https://github.com/Waltham-Data-Science/empty-ontology

Issue Tracker

https://github.com/Waltham-Data-Science/empty-ontology/issues

Contribution Guidelines

https://github.com/Waltham-Data-Science/empty-ontology/blob/main/CONTRIBUTING.md

Ontology Download Link

https://github.com/Waltham-Data-Science/empty-ontology/blob/main/empty.owl

Contact Name

Andrea Gaede

Contact Email

[email protected]

Contact GitHub Username

andreagaede

Contact ORCID Identifier

0000-0002-1909-7004

Formats

  • [x] OWL RDF/XML (.owl)
  • [x] OBO (.obo)
  • [x] OBO Graph JSON (.json)

Dependencies

  • uberon
  • cl
  • ro
  • pato
  • omo

Related

UBERON, CL, PATO

Usages

- user: https://www.ndi-cloud.com/
  description: NDI cloud uses EMPTY to annotate neurophysiology experiments

Intended Use Cases and/or Related Projects

We intend that EMPTY will be used in sharing and describing scientific data so that it can be more easily analyzed or viewed by humans and AIs.

Data Sources

The ontology is built from suggestions from scientists and curators who need to share data according to FAIR standards.

Additional comments or remarks

No response

OBO Foundry Pre-registration Checklist

  • [x] I have read and understood the registration process instructions and the registration checklist.
  • [x] There is no other ontology in the OBO Foundry which would be an appropriate place for my terms. If there were, I have contacted the editors, and we decided in mutual agreement that a separate ontology is more appropriate.
  • [x] My ontology has a specific release file with a version IRI and a dc:license annotation, serialised in RDF/XML.
  • [x] My identifiers (classes and properties IRIs) are formatted according to the OBO Foundry Identifier Policy
  • [x] My term labels are in English and conform to the OBO Foundry Naming Conventions
  • [x] I understand that term definitions are key to understanding the intentions of a term, especially when the ontology is used in curation. I made sure that a reasonable majority of terms in my ontology--and all top level terms--have definitions, in English, using the IAO:0000115 property.
  • [x] For every term in my ontology, I checked whether another OBO Foundry ontology has one with the same meaning. If so, I re-used that term directly (not by cross-reference, by directly using the IRI).
  • [x] For all relationship properties (Object and Data Property), I checked whether the Relation Ontology (RO) includes an appropriate one. I understand that aligning with RO is an essential part of the overall alignment between OBO ontologies!
  • [x] For the selection of appropriate annotation properties, I looked at OMO first. I understand that aligning ontology metadata and term-level metadata is essential for cross-integration of OBO ontologies.
  • [x] If I was not sure about the meaning of any of the checkboxes above, I have consulted with a member of the OBO Foundry for advice, e.g., through the obo-discuss Google Group.
  • [x] The requested ID space does not conflict with another ID space found in other registries such as the Bioregistry and BioPortal, see here for a complete list.

andreagaede avatar Jul 01 '25 13:07 andreagaede

Dear @andreagaede,

Thank you for your submission. The review will be executed as a two-stage process:

  • First, you will have to pass OBO NOR Dashboard. Pass means that no check apart from Users and Versioning, may be red.
  • After you have successfully passed the Dashboard, you will be assigned an OBO Operations committee member to review the ontology. The assigned reviewer is to be considered the final arbiter of requirements; look to that reviewer's guidance regarding which suggestions made by other reviewers must be done, which suggestions are simply good to do but not required, and which should not be done.

Typically, the review will provide an opportunity for you to enhance the ontology. When the reviewer believes the ontology is ready for presentation to the OBO Operations Committee, they will present your ontology during an OBO Operations Call. This allows other committee members to assess your work.

When the committee reaches a decision, you will be informed here on the issue tracker. The process can take any number of weeks or months, depending on the specific case. Please let us know if there are any reasons you have for increased urgency.

You will be informed once your ontology is loaded in the OBO NOR Dashboard.

Good luck!

anitacaron avatar Jul 04 '25 20:07 anitacaron

Dear @andreagaede,

Your ontology has been added to the OBO NOR Dashboard.

anitacaron avatar Jul 08 '25 17:07 anitacaron

Thanks @anitacaron -- I thought that I fixed the license and versioning errors, but that doesn't seem to be reflected in the dashboard. Should that be automatic? I have the following annotation: Annotation(dcterms:license https://creativecommons.org/licenses/by/4.0/) and a comment with usage terms, but it is still showing an X.

andreagaede avatar Jul 10 '25 20:07 andreagaede

The NOR Dashboard only updates on Mondays, you can check it on Tuesday.

anitacaron avatar Jul 11 '25 17:07 anitacaron

Thanks @anitacaron! I think that the NOR is passing (Versioning and Users are excepted at this stage?). Can you move forward with step 3 and following please? https://obofoundry.org/docs/SOP.html#NOR

jamesaoverton avatar Jul 22 '25 16:07 jamesaoverton

@andreagaede,

The ontology is missing logical axioms in the classes. There's only a taxonomy. Is this correct? We would like to see more. The ontology includes many RO relationships, but they are not being used.

Here's the lexical matching result for EMPTY:

Lexical matching returned results

Lexical matching returned no results

  • EMPTY:00000090 Behavioral measurement
  • EMPTY:00000091 Elevated plus maze measurement
  • EMPTY:00000093 Fear Conditioning measurement
  • EMPTY:00000094 Acoustic Startle Response derived measurement
  • EMPTY:00000100 Elevated Plus Maze: open arm (north) - entries
  • EMPTY:00000101 Elevated Plus Maze: open arm (south) - entries
  • EMPTY:00000102 Elevated Plus Maze: open arm total entries
  • EMPTY:00000103 Elevated Plus Maze: open arm (north) - head entries
  • EMPTY:00000104 Elevated Plus Maze: open arm (south) - head entries
  • EMPTY:00000105 Elevated Plus Maze: open arm total head entries
  • EMPTY:00000106 Elevated Plus Maze: open arm (north) - time
  • EMPTY:00000107 Elevated Plus Maze: open arm (south) - time
  • EMPTY:00000108 Elevated Plus Maze: open arm total time
  • EMPTY:00000109 Elevated Plus Maze: open arm total - percent time during test duration
  • EMPTY:00000110 Elevated Plus Maze: open arm (north) - latency to first entry
  • EMPTY:00000111 Elevated Plus Maze: open arm (south) - latency to first entry
  • EMPTY:00000112 Elevated Plus Maze: open arm total latency to first entry
  • EMPTY:00000113 Elevated Plus Maze: open arm (north) - time moving towards
  • EMPTY:00000114 Elevated Plus Maze: open arm (south) - time moving towards
  • EMPTY:00000115 Elevated Plus Maze: open arm total time moving towards
  • EMPTY:00000116 Elevated Plus Maze: open arm (north) - time freezing
  • EMPTY:00000117 Elevated Plus Maze: open arm (south) - time freezing
  • EMPTY:00000118 Elevated Plus Maze: open arm total time freezing
  • EMPTY:00000119 Elevated Plus Maze: closed arm (west) - entries
  • EMPTY:00000120 Elevated Plus Maze: closed arm (east) - entries
  • EMPTY:00000121 Elevated Plus Maze: closed arm total entries
  • EMPTY:00000122 Elevated Plus Maze: closed arm (west) - head entries
  • EMPTY:00000123 Elevated Plus Maze: closed arm (east) - head entries
  • EMPTY:00000124 Elevated Plus Maze: closed arm total head entries
  • EMPTY:00000125 Elevated Plus Maze: closed arm (west) - time
  • EMPTY:00000126 Elevated Plus Maze: closed arm (east) - time
  • EMPTY:00000127 Elevated Plus Maze: closed arm total time
  • EMPTY:00000128 Elevated Plus Maze: closed arm total - percent time during test duration
  • EMPTY:00000129 Elevated Plus Maze: closed arm (west) - latency to first entry
  • EMPTY:00000130 Elevated Plus Maze: closed arm (east) - latency to first entry
  • EMPTY:00000131 Elevated Plus Maze: closed arm total latency to first entry
  • EMPTY:00000132 Elevated Plus Maze: closed arm (west) - time moving towards
  • EMPTY:00000133 Elevated Plus Maze: closed arm (east) - time moving towards
  • EMPTY:00000134 Elevated Plus Maze: closed arm total time moving towards
  • EMPTY:00000135 Elevated Plus Maze: closed arm (west) - time freezing
  • EMPTY:00000136 Elevated Plus Maze: closed arm (east) - time freezing
  • EMPTY:00000137 Elevated Plus Maze: closed arm total time freezing
  • EMPTY:00000138 Elevated Plus Maze: center - entries
  • EMPTY:00000139 Elevated Plus Maze: center - head entries
  • EMPTY:00000140 Elevated Plus Maze: center - time
  • EMPTY:00000141 Elevated Plus Maze: center - percent time during test duration
  • EMPTY:00000142 Elevated Plus Maze: center - latency to first entry
  • EMPTY:00000143 Elevated Plus Maze: center - time moving towards
  • EMPTY:00000144 Elevated Plus Maze: center - time freezing
  • EMPTY:00000145 Elevated Plus Maze: test identifier
  • EMPTY:00000148 Fear-Potentiated Startle: baseline acoustic startle response amplitude
  • EMPTY:00000153 Fear-Potentiated Startle: trial type identifier
  • EMPTY:00000154 Fear-Potentiated Startle: apparatus chamber identifier
  • EMPTY:00000155 Experimental group code
  • EMPTY:00000156 Acoustic Startle Response: number of samples
  • EMPTY:00000157 Acoustic Startle Response: sampling rate
  • EMPTY:00000158 Acoustic Startle Response: startle window onset amplitude
  • EMPTY:00000159 Acoustic Startle Response: maximum amplitude
  • EMPTY:00000160 Acoustic Startle Response: time to maximum amplitude
  • EMPTY:00000161 Acoustic Startle Response: average amplitude
  • EMPTY:00000162 Experiment trial execution timestamp
  • EMPTY:00000163 Fear-Potentiated Startle: experimental phase or test name
  • EMPTY:00000164 Elevated Plus Maze: test duration
  • EMPTY:00000165 Data exclusion flag
  • EMPTY:00000168 Investigator-defined cell type
  • EMPTY:00000169 Type I BNST neuron
  • EMPTY:00000170 Type III BNST neuron
  • EMPTY:00000171 Optogenetic Tetanus Stimulation Target Location
  • EMPTY:0000146 Subject local identifier
  • EMPTY:0000149 Session Timeline
  • EMPTY:0000150 Postnatal day
  • EMPTY:0000151 Microelectrode voltage offset
  • EMPTY:10000001 Treatment: Experienced cricket hunting
  • EMPTY:10000002 Treatment: Has not experienced cricket hunting
  • EMPTY:10000003 Treatment: Acclimation onset time
  • EMPTY:10000004 Treatment: Acclimation temperature
  • EMPTY:10000005 Treatment: Non-survival experiment time
  • EMPTY:10000006 Treatment: Left eye premature eye opening
  • EMPTY:10000007 Treatment: Right eye premature eye opening
  • EMPTY:10000008 Treatment: Natural left eye opening
  • EMPTY:10000009 Treatment: Natural right eye opening
  • EMPTY:10000010 Treatment: Grating direction-of-motion visual stimulation
  • EMPTY:10000011 Treatment: CNO or saline administration
  • EMPTY:20000001 Purpose: Assessing spatial frequency tuning
  • EMPTY:20000002 Purpose: Assessing temporal frequency tuning
  • EMPTY:20000003 Purpose: Assessing direction of motion tuning
  • EMPTY:20000004 Purpose: Assessing contrast tuning
  • EMPTY:20000005 Purpose: Assessing ocular dominance or binocular matching
  • EMPTY:20000006 Purpose: Assessing the pyloric rhythm
  • EMPTY:20000007 Purpose: Assessing the gastric mill rhythm
  • EMPTY:20000008 Purpose: Assessing activity with temperature manipulation
  • EMPTY:30000001 Approach: Left eye view blocked
  • EMPTY:30000002 Approach: Right eye view blocked
  • EMPTY:30000003 Approach: Command temperature constant
  • EMPTY:30000004 Approach: Command temperature start
  • EMPTY:30000005 Approach: Command temperature end
  • EMPTY:30000006 Approach: Before optogenetic tetanus
  • EMPTY:30000007 Approach: After optogenetic tetanus
  • EMPTY:30000008 Approach: Before artificial visual stimulation
  • EMPTY:30000009 Approach: After artificial visual stimulation

anitacaron avatar Jul 23 '25 19:07 anitacaron

@anitacaron When I look at it on Protege, the terms that are listed under "Lexical matching returned no results" are all subclasses of classes listed in the top half of your list -- or nested further in some cases. They all say "SubClass Of" something. Is this not correct?

andreagaede avatar Jul 23 '25 20:07 andreagaede

I took a quick look at this and note that this fails Principle 12 (https://obofoundry.org/principles/fp-012-naming-conventions.html) with respect to term names. Please see the third bullet point under 'Details' on that page, noting the capitalization rules. Basically, all terms should be lowercase, with some exceptions.

nataled avatar Aug 05 '25 16:08 nataled

@andreagaede, the terms under "Lexical matching returned no results" indicate that the lexical tool couldn't find another match, which is good for this case. However, the "returned results" list is one you should have a look at. Following Principle 10, we recommend importing terms that already exist in other ontologies.

anitacaron avatar Aug 05 '25 17:08 anitacaron

I performed the non-technical review. The submitted ontology is unconnected to any prior work done in OBO. The terms are not placed within the BFO or COB hierarchy, and there are no logical definitions linking the terms to anything at all. So, overall, this is a stand-alone artifact, and it is completely unclear why the submitter would want this in the OBO community.

Submitter said that "There is no other ontology in the OBO Foundry which would be an appropriate place for my terms. If there were, I have contacted the editors, and we decided in mutual agreement that a separate ontology is more appropriate." This is wrong, there is massive overlap in scope for the whole ontology - but the ontology just chooses to ignore all prior work, so it does not show up in the technical tests.

Based on the above, I do not think the ontology should be admitted to OBO. I would recommend the submitters to either 1) work on their own stand-alone needs and ignore this feedback, or 2) if they want to actually work on FAIR date representation, completely revisit how they are representing their information and align it with existing OBO work.

bpeters42 avatar Aug 06 '25 23:08 bpeters42

Hi @bpeters42 -

Thanks for your review of our ontology. I appreciate that you don't see the fit with OBO, but I don't really follow the reasoning why. In our work, we use our ontology alongside Uberon and Cell ontology and PATO to describe experimental data, so it seems be part of the greater constellation of terms needed to specify biological metadata. Maybe you can help clarify so we (@andreagaede and I) understand better.

there is massive overlap in scope for the whole ontology - but the ontology just chooses to ignore all prior work, so it does not show up in the technical tests

It is not our intention to ignore prior work. Can you give an example? We are unaware of ontologies that try to characterize the purposes of measurements or single terms to capture experimental treatments or specific behavioral measurements, etc. We use RO to describe the relationships among these terms. This is a category of metadata that we have not encountered elsewhere, yet we have found it critical to documenting biological experimental data in a way that makes it easy to find by these terms.

We use this ontology alongside many OBO ontologies, some of which name phenotypes or body parts or cell types or relations. We anticipate we will use OMO to specify many units of measure. Because we need these terms, in addition to many other OBO ontology terms, we felt it made sense for it to be a part of the broader community.

Thanks Steve

stevevanhooser avatar Aug 19 '25 01:08 stevevanhooser

One more note @bpeters42, I realized I could do better explaining how we integrate with OBO ontologies.

One application we have is annotating data from scientific papers. In physiology, investigators often divide their cells into putative "classes" based on response properties to stimulation or responses to current injection or other properties. It's important that we annotate the recordings from these cells as being from the investigator-defined classes.

We have a term EMPTY:00000168 (investigator-defined cell type) from which we can define instances.

Here we defined one such term, using UBERON to indicate where it is in the brain:

id: EMPTY:00000169
name: type I BNST neuron
def: "A type of neuron located in the dorsolateral bed nucleus of the stria terminalis (BNSTDL) that fires regularly, displays moderate spike frequency adaptation, and exhibits a voltage sag indicating the presence of the hyperpolarization-activated cation current (Ih). [Source: https://doi.org/10.1016/j.celrep.2025.115768]" []
is_a: EMPTY:00000168 ! investigator-defined cell type
is_a: UBERON:0001880 ! bed nucleus of stria terminalis
property_value: IAO:0000118 "BNSTNeuronTypeI" xsd:string

One might ask, why not just put this type in cell ontology? The reason is that the cell ontology is for cell types that have extraordinary consensus on the basis of molecular, anatomical, and ontogenic criteria.

Yet, these investigator-defined terms are rigorous and need to be tagged for search and for association with the raw data that was collected.

Our ontology is really focused on what is needed to annotate data from individual studies as completely as possible but also in as general as a way possible and using the OBO tools. We find we need a lot of these "middle" terms in order to succeed.

Best Steve

stevevanhooser avatar Aug 19 '25 19:08 stevevanhooser

The relationship to the UBERON term for EMPTY:00000169 should not be is_a, but rather 'located in'.

addiehl avatar Aug 19 '25 21:08 addiehl

Thanks Alex. Steve: You are simply not following any OBO design patterns.

On Tue, Aug 19, 2025 at 5:18 PM Alexander Diehl @.***> wrote:

addiehl left a comment (OBOFoundry/OBOFoundry.github.io#2753) https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2753#issuecomment-3202262487

The relationship to the UBERON term for EMPTY:00000169 should not be is_a, but rather 'located in'.

— Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2753#issuecomment-3202262487, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJX2IW54TT3RVTFTZD5E333OOIA3AVCNFSM6AAAAACARFSKCSVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZTEMBSGI3DENBYG4 . You are receiving this because you were mentioned.Message ID: @.***>

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bpeters42 avatar Aug 19 '25 21:08 bpeters42

@bpeters42 -

Design patterns meaning governance or software? We'd like to get it right. Is there a place in the community where we can go for some advice on correcting the deficiencies / differences?

Thanks Steve

stevevanhooser avatar Aug 19 '25 23:08 stevevanhooser

@addiehl Thanks Alex

stevevanhooser avatar Aug 19 '25 23:08 stevevanhooser

There are many papers on ontology design patterns. For a practical example from the Ontology for Biomedical Investigations (OBI), you could look at this paper "Standardization of assay representation in the Ontology for Biomedical Investigations." For an applied example of the OBI assay design pattern, you could look at this paper, "MRIO: the Magnetic Resonance Imaging Acquisition and Analysis Ontology."

The recent preprint on the Cell Ontology, "The Cell Ontology in the age of single-cell omics," shows some common design patterns for cell types in Figure 5.

addiehl avatar Aug 20 '25 02:08 addiehl

Thanks @addiehl and @bpeters42

So what we (@andreagaede and I) are gathering is that our "purposes" can be expressed as comments on some concepts present in OBI. While we have some errors in our relations that we can fix there are also some terms from OBI that we can integrate. (For example, a "purpose" of measuring the membrane resistance of a cell might be a comment on an electrophysiological recording where many measurements were made, including a measurement of membrane resistance, since many time series recordings don't have single purposes.)

We have some questions, for example, if we have a microscope taking photographs of a subject, is each photograph considered an "assay" in OBI or is it some smaller unit. Where can we ask these types of questions? OBO slack? Is there a good channel?

Thanks Steve

stevevanhooser avatar Aug 20 '25 12:08 stevevanhooser

The assay is the planned process involved in taking the photograph. In general assays are processes that produce some instance of data of a particular type as output. The photograph is an instance of data, an 'image data set' (OBI:0003354).

You might consider reading the original OBI paper as well: "The Ontology for Biomedical Investigations."

If you are truly interested in learning about ontology from a more formal perspective, the following book is a good place to start "Building Ontologies with Basic Formal Ontology."

addiehl avatar Aug 21 '25 03:08 addiehl

@stevevanhooser I reached out to you on slack to continue the discussion there!

matentzn avatar Aug 21 '25 11:08 matentzn

@matentzn continuing the discussion on Slack? Bear in mind we'll lose all record of it. I personally think it is a bad idea, but if you (a) let everyone know where that discussion is being held, and (b) summarize or reproduce that discussion here, I guess it isn't so bad.

Edit: My comments apply to discussions specific to this ontology. Any discussions of a more general sort should be fine there without follow-up here. I do have a concern that the general discussion will bleed into specifics though.

nataled avatar Aug 21 '25 14:08 nataled

@matentzn continuing the discussion on Slack? Bear in mind we'll lose all record of it. I personally think it is a bad idea, but if you (a) let everyone know where that discussion is being held, and (b) summarize or reproduce that discussion here, I guess it isn't so bad.

Sorry, I meant regarding this item (and only that):

We have some questions, for example, if we have a microscope taking photographs of a subject, is each photograph considered an "assay" in OBI or is it some smaller unit. Where can we ask these types of questions? OBO slack? Is there a good channel?

We wont discuss the ontology on slack at all, or at least I wont! But you are right to call it out, we should have any discussion relevant to the development of this ontology here on the PR of course.

matentzn avatar Aug 21 '25 15:08 matentzn

OK, I'll ask a few more general questions here. We'll move our most technical questions off.

@addiehl thanks for the paper on the OBI, that's helpful. I see the structure and understand how it can be used in many applications. I wasn't aware of that paper or that ontology previously.

@addiehl and @bpeters42 - are there metadata standards that use OBI terms in their datasets? I've looked at the IEDB and EuPathDB, cited in the paper, and downloaded a couple of datasets. I did not look at many datasets, but the datasets I did look at were not highly annotated and didn't seem to use OBI terms. I'm not very knowledgeable about these types of studies, so I likely have looked in the wrong places. I was expecting to find documents or other metadata that referred to the nodes in OBI.

For example, in our software, we have subjects that can have species, and a user has to specify the species with some ontology node (such as NCBITaxon). Our data standards are outside the ontology, but they require referring to a supported ontology term for many entries.

I understand the OBI terminology schema (I'm still learning but to first order I understand it), and I can already see where some of our terms could inherit from OBI, but I am looking for examples about how it has been applied in data files to describe datasets.

(We annotate physiology data, where multiple acquisition devices are turned on and off during an assay, the user might decide to use triggered acquisition one day and continuous the next day; where they might change the camera during the course of the study, etc. So any "assay" or "process" has to be quite flexible and doesn't generate the same data structures every day.)

Seeing an application and the data files and standards that reference the OBI ontology would help a lot, particularly seeing an example dataset instance of those files.

Thanks Steve

stevevanhooser avatar Aug 21 '25 15:08 stevevanhooser

A quick way to see OBI use in the IEDB is by looking at the specific assay records (which is the most basic unit of data in the IEDB). There are >2 Mio of them.

https://www.iedb.org/assay/1505273

I hope it is self explanatory. The references to ontology terms are in the rightmost column in a namespace:ID format. For those values, the middle column has the ontology term label.

I can go into much more detail if needed.

On Thu, Aug 21, 2025 at 11:41 AM Steve Van Hooser @.***> wrote:

stevevanhooser left a comment (OBOFoundry/OBOFoundry.github.io#2753) https://github.com/OBOFoundry/OBOFoundry.github.io/issues/2753#issuecomment-3211147540

OK, I'll ask a few more general questions here. We'll move our most technical questions off.

@addiehl https://github.com/addiehl thanks for the paper on the OBI, that's helpful. I see the structure and understand how it can be used in many applications. I wasn't aware of that paper or that ontology previously.

@addiehl https://github.com/addiehl and @bpeters42 https://github.com/bpeters42 - are there metadata standards that use OBI terms in their datasets? I've looked at the IEDB and EuPathDB, cited in the paper, and downloaded a couple of datasets. I did not look at many datasets, but the datasets I did look at were not highly annotated and didn't seem to use OBI terms. I'm not very knowledgeable about these types of studies, so I likely have looked in the wrong places. I was expecting to find documents or other metadata that referred to the nodes in OBI.

For example, in our software, we have subjects that can have species, and a user has to specify the species with some ontology node (such as NCBITaxon). Our data standards are outside the ontology, but they require referring to a supported ontology term for many entries.

I understand the OBI terminology schema (I'm still learning but to first order I understand it), and I can already see where some of our terms could inherit from OBI, but I am looking for examples about how it has been applied in data files to describe datasets.

(We annotate physiology data, where multiple acquisition devices are turned on and off during an assay, the user might decide to use triggered acquisition one day and continuous the next day; where they might change the camera during the course of the study, etc. So any "assay" or "process" has to be quite flexible and doesn't generate the same data structures every day.)

Seeing an application and the data files and standards that reference the OBI ontology would help a lot, particularly seeing an example dataset instance of those files.

Thanks Steve

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

bpeters42 avatar Aug 21 '25 21:08 bpeters42

Thanks @bpeters42, it will take a week or so for us to study but we'll get back to you all soon.

stevevanhooser avatar Aug 27 '25 09:08 stevevanhooser

Hi @stevevanhooser, could you provide an update following @bpeters42 last comments? Are there any developments or challenges you'd like to share?

pfabry avatar Sep 18 '25 18:09 pfabry

Hi @pfabry - we are still interested but it might be a couple more weeks before we have time to incorporate the changes just due to other deadlines. Best Steve

stevevanhooser avatar Sep 21 '25 22:09 stevevanhooser

Hi @stevevanhooser, were you able to make any progress on the update?

pfabry avatar Oct 14 '25 16:10 pfabry

Thanks for asking @pfabry . We have a major conference beginning the week of Nov 15, and then the American Thanksgiving holiday, after which time this will move to the front for us. Thanks for your patience. Best Steve

stevevanhooser avatar Nov 03 '25 12:11 stevevanhooser

Hi @stevevanhooser, Could we get a status update on the ontology advancement? To keep the issue tracker organized, feel free to close this for the time being if work is on hold. We can reopen it at your convenience.

pfabry avatar Jan 05 '26 15:01 pfabry