data2health/contributor-role-ontology

This ontology provides contribution roles for use in crediting persons or organizations.

contributor-role-ontology's Issues

NTR: object acquisition role

For new term requests, please provide the following information:

Preferred term label

object acquisition role

Synonyms

(e.g., Absent spleen)

Textual definition

a contributor role wherein the bearer collects physical objects for research purposes

Suggested parent term

contributor role

Attribution

http://orcid.org/0000-0002-2908-3327

Develop a CRO Contribution Data Model

It was recently proposed that we develop a data model specification based on the CRO to support clear and concise representation of contributions made by agents to research artifacts. I am starting this ticket to initiate this work (although it will likely end up in its own repo?).

I created two documents to get things started:

1. A Project Plan that outlines deliverables required to meet short term project requirements.
2. An Information Model Proposal that presents a candidate model, compares it to related efforts, and provides an exemplar dataset demonstrating the model's application to an example contribution scenario.

@mellybelly @marijane @nicolevasilevsky @kristiholmes @LisaOKeefe1 please review these documents, edit/comment as desired, and we can follow up with a call as needed.

IAO import side effects

I imported the IAO ontology metadata namespace in order to get access to annotations like obo:definition. The corresponding classes for these properties show up in the class tree in Protege. I'm not clear if this is something I should work around with a MIREOT of this namespace.

CRO_00000000 has one more digit in its ID than the rest of the classes

It was generated by the ontology-starter-kit, and I failed to notice until after I'd added the CRediT roles. I think most of the OBO ontologies I've looked at use 7 digits.

Should we bump all the identifiers up to 8 digits or knock this one down to 7?

Integrating with other ontologies

For now I have implemented this as a standalone ontology, but we should discuss whether we want it to import BFO and descend from obo:Role, and whether this can be done in a modular/optional way.

Should CASRAI be included in annotations as a term editor?

They authored the terms, it feels appropriate to give them some kind of editor credit beyond the existing definition source annotations that point to entries in the CASRAI dictionary.

add synonym to 'formal analysis role'

data analysis role

Clarify 'resource role'

The 'resources role' is defined from the perspective of a project or publication to which an agent provides a research resource: "Provision of study materials, reagents, materials, patients, laboratory samples, animals, instrumentation, computing resources, or other analysis tools".

If I want to capture the fact that an agent was the creator of a physical resource, e.g. a transgenic mouse, what role would I use? The 'resources role' doesn't fit because it describes the provision of the resource as opposed to its creation. There is no generic 'creator role', nor are there more specific roles describing contributions to physical artifacts - as there are for contributions to software, data artifacts, and publications in the 'data role', 'software role', and 'author role' hierarchies, respectively.

Some thought needs to go into how to support such use cases, and how to treat roles around generation of physical resources in relation to how we have treated roles around informational resources.

add synonym to 'funding acquisition role'

grant acquisition role

@mellybelly @marijane @kristiholmes
let me know if there are any objections

Should contribution roles be object properties?

if we are to use them in triples
person <-contribution role-> artifact
we will need to figure out the best practice for doing so.

Reconsider import of credit-ontology vs MIREOT

I refactored CRO to import credit-ontology because it was so small, MIREOT seemed silly.

It introduced two problems, however:

• Two root contributor role classes
• Locking us into the credit-ontology class hierarchy

If we revert to using MIREOT, that would eliminate both of these problems, and I'm not sure there's any downside.

Map research outputs to existing ontology terms

Per our meeting at Rocky, I will map research outputs from NISO to existing ontology terms in this spreadsheet: https://docs.google.com/spreadsheets/d/1Mw8gK2NUGM8po7GGRtJTShRM2QNFoR19VJrjQuVCDW8/edit#gid=1619162717

NTR: collector role

For new term requests, please provide the following information:

Preferred term label

Collection role

Synonyms

Textual definition

Activities to obtain physical objects for research purposes or to add to a collection

Suggested parent term

contributor role

Attribution

0000-0002-2908-3327

Notes

Current collector role applies only to data

clarify software design role

Please add a definition. It's not clear where this fits and how it does not overlap with other software related roles.

NTR: presenter role

For new term requests, please provide the following information:

Preferred term label

presenter role

Synonyms

presentation role
lecture role
lecturer role

Textual definition

Oral presentation intended to present information or teach people about a particular subject, such as a talk or poster presentation at a conference.
Source: https://www.wikidata.org/wiki/Q603773

Suggested parent term

'contributor role'

I am mapping personas roles to CRO and I can't map 'conference presentations and posters'. Does this seem like an appropriate role?

Model "degree of contribution" as described in the FAQ?

Per the CRediT FAQ:
"When there are multiple people serving in the same role a ‘degree of contribution’ should be further specified as either ‘lead’, ‘equal’, or ‘supporting’. "

Should we include this concept in the ontology? How might we model it?

NTR: peer review role

For new term requests, please provide the following information:

Preferred term label

peer review role

Synonyms

manuscript review role
grant review role

Textual definition

Evaluation of scientific, academic, or professional work, such as manuscripts or grants by others working in the same field.
Source: https://www.lexico.com/en/definition/peer_review

Suggested parent term

'contributor role'

I am open to suggestions/feedback on this request, not sure if this is the best term. In the personas, there is a person who reviews manuscripts for NIH study section, I am not sure which role to give him, I don't think we have anything that currently fits, hence I am suggesting this new term.

obsolete CRO_0000088 'original draft preparation role'

Per Matt's review, (#31), CRO_0000088 'original draft preparation role' and CREDIT_00000013 'writing original draft role' are almost identical.

I suggest we obsolete CRO_0000088 'original draft preparation role' and move CREDIT_00000013 'writing original draft role' to be a child of 'author role'.

issues with saving when I edit superclass for writing original draft role

I want to reclassify writing original draft role to be a child of 'author role'. When I change the superclass to be 'author role', it won't let me save the file, when I click 'save', it behaves like I am doing 'save as'

suggested def: 'graphic design role'

A communication role that utilizes the art or profession of using design elements (such as typography and images) to convey information, create visualizations, or create an effect.

source: https://www.merriam-webster.com/dictionary/graphic%20design

add definitions to CRO terms lacking text defs

Marijane did a SPARQL query and created a list of all the CRO terms that are missing definitions:
https://docs.google.com/spreadsheets/d/1QqKUtSQ701gq1bwEY2EF-8FrYnZUlCRvW3V0PY02euM/edit#gid=0

If anyone has suggested defs, please add them here.

move definition source to an annotation on the definition

to do

I will do this after the recent PRs are merged

suggested def for data aggregation role

Preferred term label

data aggregation role

Textual definition

The compiling of information with intent to prepare combined datasets for data processing.

Source: Stanley, Jay; Steinhardt, Barry (January 2003). "Bigger Monster, Weaker Chains: The Growth of an American Surveillance Society". American Civil Liberties Union.
(This is from wikipedia: https://en.wikipedia.org/wiki/Data_aggregation)

Note, I revised this def slightly.

please comment on this def. I'll add it on a branch/create a pull request and it can be updated, if needed.

suggested def: Community engagement role

A communication role which involves the dynamic relational process that facilitates communication, interaction, involvement, and exchange between an organization and a community for a range of social and organizational outcomes.

source: Johnston, K. A. (2018). Toward a theory of social engagement. In K. A. Johnston & M. Taylor (Eds.), The Handbook of Communication Engagement (pp. 19-32). Hoboken, NJ: Wiley.

reclassify CREDIT_00000002 'data curation role'

should CREDIT_00000002 'data curation role' be a child of CRO_0000015 data role?

NTR: acquisition role

For new term requests, please provide the following information:

Preferred term label

acquisition role

Synonyms

Textual definition

See discussion #82
Selecting, ordering, and receiving materials or physical objects for research, scholarly, library or archival collections.

Suggested parent term

collector role

Attribution

orcid.org/0000-0002-2908-3327

Clarify name/purpose of the 'author role' grouping

The name 'author role' suggests that all roles captured for authors of a publication should come from this hierarchy. But this is not the case. Roles for publication authors can come from anywhere in the CRO - and indeed many of the original CREDIT roles meant for capturing contributions to pubs are not in the author role hierarchy (e.g. visualization role, resource provider role)

As the roles in the current 'author role' hierarchy are mainly related to preparation of the publication itself, consider renaming this to 'publication preparation role'? Or minimally, if the name is not changed, add some metadata that makes the purpose of this class clear, and that roles captured for authors of a publication can come from anywhere in the CRO.

NTR: primary collector role

For new term requests, please provide the following information:

Preferred term label

primary collector role

Synonyms

Textual definition

In botany, this is the collector listed first for a particular specimen. Each specimen has one primary collector. The primary collector assigns a number to that specimen from his/her own number series.

Suggested parent term

specimen collection role

Attribution

http://orcid.org/0000-0002-2908-3327

NTR: specimen collection role

For new term requests, please provide the following information:

Preferred term label

specimen collection role

Synonyms

Textual definition

See discussion #82
Obtaining a material entity for potential use as an input during an investigation.

Suggested parent term

collection role

Attribution

orcid.org/0000-0002-2908-3327

computer programming role

According to the definition, this includes requirements analysis. I think requirements analysis is a separate activity, so I propose a new term, requirements analysis role. The person who does the programming is not always the person who does the requirements analysis.

question: alt term for CREDIT_00000001 conceptualization role

@marijane I added an alt term to CREDIT_00000001 conceptualization role: research conceptualization role

I did this in the cro-edit.owl file, but realized maybe this change should have been made in the imported credit.owl file?

Include CASRAI IDs in class annotations

Each of the CRediT Taxonomy roles has a unique ID in the CASRAI Dictionary. We should include this ID in the annotations on the role classes, but it's not clear if there is an existing OBO annotation property that should be used for this. The alternate term property does not seem quite right to me.

supervision role and team management role

I propose moving these under infrastructure role

software project management

I propose that this be a subclass of infrastructure role

review content in CRO website

the website is done and ready for review

Punctuation in labels of writing terms?

CASRAI has styled these roles as follows:

• Contributor Roles/Writing – original draft
• Contributor Roles/Writing – review & editing

I removed the punctuation from these terms, but I'm wondering if I should have left them in? I couldn't find anything in the OBO Tutorial or naming conventions that recommends anything about punctuation.

NTR: Curator role

For new term requests, please provide the following information:

Preferred term label

Curator role

Synonyms

Textual definition

Management activities to annotate, maintain, research, and preserve physical objects to maximize their use for research and education now and into the future.

Suggested parent term

contributor role

Attribution

0000-0002-2908-3327

Notes

The curator role currently in CRO appears to only apply to data. I need terms that can apply to physical objects. In addition, the preservation roles are a bit too restrictive. A curator preserves and more.

preservation role

According to the definition given, I propose changing the label to "deposition role".

ntr: project management role

For new term requests, please provide the following information:

Preferred term label

project management role

Synonyms

PM role

Textual definition

Planning, management, and monitoring of projects.

Suggested parent term

'infrastructure role'

Import oboinowl and map classes to CRediT

We want to use the OBO hasSynonym relationship to map CRO classes to credit-ontology.

User experience with Attribution Ontology in OpenVIVO

I used an older version of the attribution ontology in OpenVIVO. Overall, it worked very well. However, there were some instances where the output was a solo effort, and it felt rather uncomfortable to choose so many roles. Other times the output was part of a collaborative effort, and I wasn't sure if I could assume the role of "project management" when it was a team effort, even though I felt I really moved things along. Whereas, the less leadership focused roles were easier to select and didn't require as much deliberation on my part. These experiences might be part of human nature and unavoidable when interacting with a contributor role ontology. But I do wonder if providing examples or short definitions might mitigate some of that anxiety.

technical writing role

I propose making this a subclass of documentation role

Clarify similar classes

What is the difference between:
systems administrator role and systems administration role
project administrator role and program administration role
supervision role and supervisory role

ORCiDs for term editor values?

I entered my name as a string in the term editor annotations, but I'm wondering whether it's appropriate to use an ORCiD as the value for this property.

suggested def: documentation role

A communication role in which one records the details of an event, a process, a workflow, etc.

source:
https://dictionary.cambridge.org/us/dictionary/english/document

NTR: collection role

For new term requests, please provide the following information:

Preferred term label

collection role

Synonyms

Textual definition

see discussion in #82
Collection of physical objects for research or scholarly purposes.

Suggested parent term

contributor role

Attribution

http://orcid.org/0000-0002-2908-3327

create a CRO webpage

@marijane suggested we create a GitHub website for the CRO, which includes an editors guide (which would include annotation conventions), and an FAQ page.

Various suggestions for improving definitions and labels

Hi. Reporting a handful of minor issues i noted on reviewing the CRO - mostly concerning definitions and labels. Happy to split these out int separate tickets if you want - just say the word.

• 1. As noted by others, a challenge in evaluating the ontology is that so many terms lack definitions - and many that exist are not sufficiently discriminating. This can make it hard to evaluate how some terms are different from each other, and if their classification makes sense. I would make adding defs a top priority - and making sure the defs are clear and precise to distinguish between classes. Also, be sure to include a definition for the root 'contributor role' class as well, and perhaps some clarifying comments- to provide a foundational understanding of what we mean by a 'contribution' in general. See #32

• 2. 'Author role' needs better definition. Currently reads "Contributions to the published research object." Defs of most children start with and then extend the phrase "Preparation, creation and/or presentation of the published work" so makes sense to use this in some way as the definition of the 'author role' parent. Also, the def or a comment should clarify the types of artifacts that are "authored" - to help scope when author roles should be used to describe creation of an artifact. e.g. is this only for things like books, journal articles, and other publications? or can things like technical documentation, web sites, code, ontologies, or data model be authored?

• 3. Other pairs of terms that are not clearly distinguished (to add to the list started by Anne in #20):

  • - 'writing original draft role' and 'original draft preparation role' - defs are nearly identical. See #52
  • - 'conceptualization role' and 'research conceptualization role' - identical definitions (one has Credit prefix and the other CRO - not sure what the relationship is here)
  • - 'educational training role' and 'educational instruction role' - lack definitions, but sound very much the same.
  • - the definition for 'program administration role' sounds like it may be the same thing as 'research coordination role' - but the latter has no definition so I cannot be sure.
  • - 'IT hardware systems design and implementation role' and 'hardware systems role' - no def for the latter, but sound similar by name.

• 4. I'd like to see a definition for 'data role' in particular, to be able to evaluate what belongs in this hierarchy of terms.

  • - e.g. things like data standards development and data modeling may not involve actually working with data - s depending on how data role is defined, these may belong elsewhere.
  • - and 'formal analysis role' and 'visualization role' needs improved definition as well - as I am not convinced these belong here either.

• 5. 'data role' > 'data visualization role' has same text definition as 'author role' > 'figure development role'. These should be clearly distinguished as they are different things. and also noticed that 'data role' > formal analysis role' also has this same definition, which is clearly a mistake.

• 6. 'Infrastructure role' is not defined, but from its context, I'm not sure I like the name of this class. Seems too generic/vague.

• 7. 'investigation role' as a label seems too generic - given that I think its intended meaning is to describe someone who actually executed experiments/computational analyses in the course of a research project. With such a generic name, I would expect to find other types of contributions to investigations here - e.g. funding acquisition role, conceptualization role, study design role, etc.
  NV: this comes from CREDIT, we would have to change the CREDIT ontology to address this. @kristiholmes or @marijane could you comment?

• 8. Rename 'resource role' to 'resource provision role'?

  • - 'resources role' is quite vague - the def seems to describe someone who provides resources used in a research project.
    NV: this comes from CREDIT, we would have to change the CREDIT ontology to address this. @kristiholmes or @marijane could you comment?

• 9. Is there a good reason that software systems role is not classified under 'software role'
  NV: Could we give classes multiple parents? @mellybelly or @marijane could you comment?

• 10. 'standards development role' sounds like it should subsume some other classes in the ontology. e.g. 'standard operating procedure development role', 'data standards developer role'
  NV: Could we give classes multiple parents? @mellybelly or @marijane could you comment?

• 11. 'validation role' could use a more specific name, given its def.
  NV: this comes from CREDIT, we would have to change the CREDIT ontology to address this. @kristiholmes or @marijane could you comment?

NTR: patient advocate role

new term request: patient advocate role

In the personas, there is someone who "serves as a "patient voice" to incorporate patient reported outcomes into trial design"

How would we annotate this role? Should we create a new role 'patient advocate role' or something like this?

cc @mellybelly @kristiholmes @marijane

need definition for data role

CRO_0000015 data role needs a definition

related to #19

See suggested defs for child terms in this spreadsheet