openrif/community

This repository is community oriented wiki and issue tracker without any code. It is the community documentation and communication channel for the OpenRIF organization.

community's Issues

Review FaBIO ontology for inclusion and possible replacement of parts of BIBO ontology

As discussed at the I-Fest, consider adding several FaBIO classes -- which immediately raises strategic decisions about whether FaBIO is enough of an improvement on BIBO that we should consider a merger or replacement. This is a good area for a task force to review publication-related ontology changes and make a recommendation.
One possible resource is a Google Doc at http://goo.gl/NKU1XR and a more detailed comparison of VIVO and BIBO with BIBFRAME and FaBIO at http://goo.gl/2zZx8G

vivo:dateFiled (domain: biboPatent)

The domain of the property vivo:dateFiled is defined as bibo:Patent.

1. My understanding on this property is that it is equivalent to "date submitted".
2. I think the domain of such a generalized property should be either kept "open" (i.e., without a domain) or a very higher-level class should be defined as its domain e.g. (obo:IAO_0000030 - Information Content Entity).

vivo:Membership

It's in the diagrams at https://wiki.duraspace.org/x/j-YQAg but apparently not in the distributed ontology

https://jira.duraspace.org/browse/VIVO-1099?filter=13110

Consider addition of ISNI as an identifier for organizations

ISNI, the International Standard Name identifier has been issued to over 446K organizations world wide. The University of Florida ISNI, for example, is 0000 0004 1936 8091. UF has extended its VIVO to allow for the capture of organizational ISNI. Seems this should be a standard part of VIVO-ISF.

Incorporate the contribution ontology in VIVO-ISF

Unclear what is involved here. The ontology is provided in OpenVIVO in a separate tbox filegraph.

Ontology needs to be at OBO? The URL used in OpenVIVO does not resolve:

http://purl.obolibrary.org/obo/cro.owl

Then can be treated as an independent ontology in VIVO, separately loadable, separately referenced in SPARQL?

Add lat and long

There are existing small standard ontologies for specifying latitude and longitude. Would be good to select one for inclusion in VIVO.

And then perhaps we need to specify a domain -- what can have a lat and long?

Add additional person identifiers

Add additional person identifiers analogous to ORCiD and eRACommons:

Twitter username
LinkedIn username
Facebook username
Google username
ResearchGate username
Academia.edu username

Add GRID ID as a data property for organizations

See https://jira.duraspace.org/browse/VIVO-1325

GRID is a popular identifier for organizations used by OpenVIVO.

Relationship(s) between funding and scholarly work?

A common need in the recording of scholarly work, prepatory to assessment and impact activities is to indicate that a work is the output of funding. So we have:

work relationship funding

where the work might be any scholarly work -- a paper, a dataset, a clinical trial, a project, a symphony, book etc. And "funding" might be any funding -- internal award, external award (grant), etc.

the relationship of primary interest is "output of" or "resulting from" as in

this paper resulted from that funding

We see these kinds of relationships in the pubmed system. There papers have "cites grant" and a list of NIH awards that helped support the production of the paper.

How should should relationships be modeled in the ISF? Do we need more elements, or are the existing elements sufficient to represent the relationships?

Virustotal via Proxy from Corporate

Hi Team,

I need to enable proxy to access the Virustotal module in Cuckoo. Now I have installed Cukoo in RHEL 7.

Where I need to provide Proxy to enable VT module in Cuckoo.?

Note: I tried using proxy in Browser, but it doesn't work.

Thank You.!

SatheeshKumar T

Representing Fellows and Fellowships

"Fellows" and "fellowships" are not clearly modeled in the VIVO-ISF. How to represent a fellow (a person with a fellowship) where a fellowship might be

an award -- a recognition for outstanding potential for scholarship
a position -- the fellowship pays the fellow and is in an organization
an educational process -- the fellowship might appear as part of the fellows training
a project -- perhaps the fellowship has an associated project

Do we have the entities needed to model fellowships with all their realizations or do we need more in the VIVO-ISF to represent fellowships properly?

Add Translatorship

Provide the ability to record translators of works. Much as we record editors and authors.

https://jira.duraspace.org/browse/VIVO-896

What ontologies/vocabularies/systems should VIVO align with?

Might be helpful to consider what ontologies/vocabularies/systems are popular/expected for VIVO to align with.

Can/should we represent everything in ORCiD? ResearchGraph (ANDS and RDA)? DataCite? CASRAI? COAR? OpenAire? Others?

In some cases, this might involve partnering, active collaboration.

Looking for the VIVO ontology

Coming from the Download Ontology menu at http://vivoweb.org, I got here. It doesn't seem that there is an owl file to download. Any suggestions?

ControlledClinicalTrial?

Should we extend OBO:ClinicalTrial to a subclass ControlledClinicalTrial? Many clinical trial classifications and training make distinctions between ClinicalTrials and ControlledClinicalTrial. OBO subclasses ClinicalTrial with the phases. It could be that the phases are either controlled uncontrolled trials.

A related issue is representing ClinicalTrials.gov studies

Revise academic degrees, create ontology

Currently VIVO has a list of academic degrees as a controlled vocabulary. Need to add to it from the experience of the VIVO community.

Degrees should be classes. Degrees people got should be individuals.

Also need to consider a higher level ontology of degrees so that we might be able to characterize degrees as "undergraduate", "graduate" "professional"

The topic of the degree might be of interest -- STEM, humanities, etc.

Consider subtypes for vivo:dateTimeValue

Several scenarios where a single dateTimeValue is either insufficient or non-informative to represent the reason for recording a date associated with an entity. Date time intervals obfuscated dates further by pushing a start and stop into a non-informatively labeled interval.

Project might have approvalDate, fundedDate, etc.

Publication might have datePublished, dateSubmitted, etc.

Grants might have dateSubmitted, dateAwarded, etc.

Patents might have dateFiled, dateApproved, etc.

Organizations might have dateEstablished

Or perhaps all these are simply dates of some action and we are not modeling the action

Add ISNI as a data property

Add ISNI as a data property. ISNI is used to identify people and organizations. Se http://isni.org

While ORCiD is a subset of the ISNI numbering space, ORCiD is treated differently in VIVO-ISF, as an object property pointing to the ORCiD URI.

See https://jira.duraspace.org/browse/VIVO-1326

Ontology 7.1 and 8.4 compatibility

I downloaded Ontology app 7.1 to connect with my Ledger Nano S. After a bit I downloaded the newer version 8.4. I am unable to see my Tokens on the newer app after I conncet with it. I could do it a few times but it didn't work after a couple of days. So I was forced to go back and use my older version whic works.
Can someone please help me resolve this issue. i would really appreciate it.
Thanks.

Data Quality Vocabulary

I believe that we should be aware of that and think about how VIVO-ISF should use it.

The W3C Data on the Web Best Practices Working Group has recently published a first draft for a Data Quality Vocabulary (DQV):
http://www.w3.org/TR/2015/WD-vocab-dqv-20150625/

Our goal is to facilitate the publication of data on the quality of datasets published on the Web. We hope such information will be made widely available, so that data re-users can be better guided in their selection of data sources.

Many people on this list have worked on linked data quality.

This new W3C work is not meant to reproduce all this work. We have rather focused on a basic framework to allow people to express the quality observations that are relevant for them, using specific vocabularies defined as DQV extensions or refinements. We consider that such a common framework would make varied quality assessments better comparable - and usable.

This draft is still open for comments, from editorial remarks to deeper criticism. The group is very keen on receiving any form of 'feedback from the market', before developing this vocabulary further.

Comments can be either posted here, or sent to the dedicated W3C mailing list [email protected].
The three co-editors (cc'ed) are also willing to receive personal emails, should you not be sure that your feedback is fit for open publication!

What ontologies should we consider using?

As the world moves forward with semantics, there will be outstanding ontologies that we should consider using. In some cases this means using the ontology rather than defining our own. In other cases, it may mean ripping out a bit of our ontology and substituting axioms better developed elsewhere.

Some examples:

• W3C Time ontology (instead of vivo:dateTime things) https://www.w3.org/TR/2017/REC-owl-time-20171019/
• W3C PROV ontology (rather than developing our own provenance ontology, whatever its flaws, PROV is often considered a given)
• Contribution Role Ontology (assuming it is a superset of CRediT, seems important to say we can make CRediT assertions)
• IAO -- should we be using more of IAO and less of other document-oriented ontologies, or more or less BIBO or more or less SPAR

Expand definition of software, uses software, and used by

The domain and range of software, uses software, and used by is currently very narrow.

For example, software/databases/protocols "used by" currently has a range of foaf:Organization. But we want to model people who use software. Can the range be broadened up to foaf:Agent or beyond?

Similarly, "uses software" has a domain of service, which precludes people using software without performing a service. Incidentally, this property has a note "# deprecated" on line 5423 of initialTBoxAnnotations.n3 in the VIVO application distribution, which appears to date back to this commit: vivo-project/VIVO@f786366.

hasCollaborator property doesn't have inverse

The property http://vivoweb.org/ontology/core#hasCollaborator doesn't have a inverse property. Is that the original idea or a bug? The property does not have any documentation that describes its intentional meaning either.

Another possible suggestion is to make this property reflexive.

Revise organization ontology

Based on the experience of the community, the organization ontology can be refined, adding more organizational types, and creating some structure for the types of organizations.

Some of the current "types" are most likely functions and might be indicated in ways other than type.

need logo

for github account and for website.

align ISNI properties with VIVO-ISF

we should review the ISNI properties between organizations and types of organizations and try to reconcile these.

Does anyone know where we can find these and/or have a contact?

Changing the name of this repository to vivo-isf to match the organization to help with typing

GitHub allows cross repository references when typing text in various places. For example, to reference an issue in this repository, you would type a hash sign followed by the issue number:
#3

To reference issues in other repositories, the reference described above has to be prefixed with user/repo then the hash and the number. The current name is too long to type and it would be easier if typing the reference is vivo-isf/vivo-isf# rather than vivo-isf/vivo-isf-data-standard#

However, currently, vivo-isf/vivo-isf# does work because we have used this name in the past for this repository and GitHub remembers this and adjusts the display accordingly. For example, the following reference appears as vivo-isf/vivo-isf-data-standard# but when typing this reference I typed vivo-isf/vivo-isf#

#3

I know this is a little confusing but what I'd prefer is that we don't rely on this automatic GitHub redirection because most users that need to reference this repository will use the current long name, not any past names, because they don't know about them. And, if this is the central issue tracker, there will be a lot of cross repository references (from all the other repositories to this one).

Contributions, credits, and data sets

The VIVO-ISF needs model, and integrate any existing work, in the areas of:

• Roles for scholarly contributions and and other scholarly products
• Credits
• Data sets

Please use this issue as a starting point for refining the above into more detailed use cases, adding related resources that should be considered, etc. We will create separate issues for each specific use case as needed.

Add domain and range to vivo:middleName

vcard:givenName and vcard:familyName both have a domain of vcard:Name. vivo:middleName does not. This makes it impossible to add a middle name to a vcard:Name in the VIVO web interface unless you specify the domain manually (or edit the name via a foaf:person editing page). Should the following domain and range be added to vivo:middleName in the ontology?

    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
    <rdfs:domain rdf:resource="http://www.w3.org/2006/vcard/ns#Name"/>

vivo:Report is too general -- need subclasses

Violeta @ the I-Fest - we need subclasses such as technical report, case report

Establish licenses for ontologies

Openrif should have clear licensing for all its work. Choose licensing, document licensing practices, build licenses into the ontologies (?). Use LICENSE files, put license information on the openrif web site.

Add language tags to text literals in ontology OWL files

Best practice is to have a language tag on all text literals that are language dependent. Some text literals are not language dependent (identifiers). These should be marked as xsd:string

By adding language tags, we position the ontology files for internationalization. Additional text values can be added for other languages with appropriate language tags. Software can then choose the appropriate language to display, given local context.

See https://jira.duraspace.org/browse/VIVO-1291

Port used for communication in between Host and VM

Hi,

I need to block all the ports in Firewall except the port which is required for communication in between the hosts and VM in Cuckoo Sandbox for file analysis.

How to identify the port used for communication in RHEL.?

Thanks in Advance.!

Satheesh T

Add W3C dataset description elements to VIVO-ISF

We need to have within VIVO-ISF the ability to describe linked datasets from each org. I suggest use of the W3C dataset description properties for this purpose. See https://github.com/W3C-HCLSIG/HCLSDatasetDescriptions

@eichmann @vioil @arademaker let us know your thoughts

Explore adding Duke's Humanities ontology to VIVO ISF

We would like to utilize Dukes humanities ontology in the VIVO application. Hence we would like it included in the ISF.
I found some notes at: https://wiki.duraspace.org/display/VIVO/Humanities+Ontology

Develop requirements and use cases for fleshing out patents in VIVO-ISF ontology

We should be able to represent US Patent data in VIVO (why?) Develop use cases and representation.

See also https://jira.duraspace.org/browse/VIVO-834

Add the CrediT taxonomy as an option for the ontology

The CRediT taxonomy is an attempt to represent attribution for various roles a person might play in a scholarly work. See http://credit.casrai.org 14 roles are named.

While the taxonomy has limitations, it can be represented in VIVO-ISF and provides an opportunity for exploring attribution -- how it is represented, managed and used in scholarly ecosystems.

This issue will track s small effort to create an extension for using CRediT in VIVO via VIVO-ISF.

Domains and namespaces for new VIVO-ISF IRIs

Going forward we need a plan for creating new IRIs. We currently have few hosts and namespaces in the vivo-isf-ontology that we can continue to use and that are to some degree under our control. purl.obolibrary.org/obo/ARG_* is an example.

Things to discuss:

1. Should we continue to use the purl.obolibrary.org domain?
2. Should we register and use the vivo-isf.org domain?
3. The VIVO community will likely contribute content with the vivoweb.org domain.
4. How do we coordinate the creation of new identifiers to avoid name clashes? This is especially a problem for numerical IRIs when working in Protege.
5. Will we consider moving any of the existing IRIs to a different namespace?

Please feel free to comment, and raise any other issues related to the creation, resolution, etc. of IRIs, especially the ones for OWL classes and properties.

Rename Government Agency to Government Oranization

Would like to consider renaming the GovernmentAgency type to GovernmentOrganization. Reasons:

1. Consistency with other organization sub-types -- researchOrganization, studentOrganization, FundingOrganization.
2. "Agency" implies a part of some larger government. See, for example http://en.wikipedia.org/wiki/Government_agency
3. As a result of the above, data managers are reticent to use GovernmentAgency to refer to the government itself, or to refer to parts of a government that do not appear to be agencies. Examples: US Senate, Government of India.

Support for localID for people and departments

Common local extensions of the ontology provide for local identifiers for people and departments. At UF these are called ufid and deptid respectively. If the ontology had a localID property, we could store these identifiers as attributes and use them to insure the thin in VIVO is the thing our enterprise system is referring to outside VIVO.

review SHARE data schema

SHAREnotify is a group we should consider alignment with/help them with.
see https://github.com/CenterForOpenScience/SHARE-Schema
http://www.share-research.org/projects/share-notify/

Define ISF -- e.g., could be misinterpreted as Integrated Science Framework

I don't see any explanation for the ISF acronym on this Github site or on the previous Google Code site -- only at http://ctsaconnect.org/about-us. Seems like the acronym should be spelled out at least once on the Github project and perhaps for each repository as well.

Assign a parent class to bibo:DocumentStatus

bibo:DocumentStatus should be asserted to be subClass of something. As it is, no subClass assertion is present, creating an orphan with respect to BFO.

See https://jira.duraspace.org/browse/VIVO-1288

Find new parent class for five Classes with parent class skos:Concept

Several entities in vivo-isf are subClass of skos:Concept. Two issues here:

1. violates the BFO principle of "realist orientation"
2. leads to visible, surprising and unhelpful collections of entities in the VIVO application -- a list of research areas (concepts) includes "Teacher of the Year Award" because Award is a subClass of skos:Concept:

The entities that are subClasss of skos:Concept are:

vivo:AcademicDegree
vivo:AwardOrHonor
obo:ARG_2000376
vivo:Credential
vivo:DateTimeValuePrecision

See https://jira.duraspace.org/browse/VIVO-1287?filter=13110

Review UF VIVO ontology extensions for issues

Here's a report on UF ontology extensions. https://goo.gl/QsUFVB Which of these, if any warrant consideration as issues for VIVO-ISF?

add a README file to the VIVO-ISF repository explaining things like the modularity, the file structure, and how the eagle-i and VIVO ontology files are created and maintained

Based on a request by Alex Viggio at the I-Fest -- a typical open source person would expect to see a README file with at least basic information about the logical organization of the repository and its relationship to the applications the ontology serves

Add a Course Offering to complement vivo:Course

Based on experience at several sites, where they need a continuant as a placeholder for the official course number and/or descriptive information independent of who teaches the course in any given semester. (Similar to Award and AwardReceipt)

Not sure where this fits under BFO – final discussion at 3/26/13 OHSU meeting touched on this but was not resolved.

https://jira.duraspace.org/browse/VIVO-1097?filter=13110