Skip to content

Fixing citation reconciliation and documentation #969

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
dgarijo merged 12 commits into from
Apr 23, 2026
Merged

Fixing citation reconciliation and documentation #969

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
12 commits
Select commit Hold shift + click to select a range
e12ff7d
Changed dockerfiledoc.md name and references to it because of OpenSSF…
andriumon Apr 21, 2026
b1fb568
Reconciliation of duplicate values in publication. Fixes #953
juanjemdIos Apr 21, 2026
c907826
Merge pull request #966 from andriumon/dev
dgarijo Apr 21, 2026
a7645e2
Fix: rename file to resolve conflict
juanjemdIos Apr 21, 2026
d557723
Merge branch 'dev' into master
juanjemdIos Apr 21, 2026
e839c0a
Apply suggestions from code review
dgarijo Apr 21, 2026
a1a0588
Apply suggestion from @dgarijo
dgarijo Apr 21, 2026
6f5fc73
Resolve review comments. Better docs explaining codemeta mapping. Dep…
juanjemdIos Apr 23, 2026
ad7d3bb
somef test failed in the last PR. But not in local.
juanjemdIos Apr 23, 2026
86646da
reset pom parser
juanjemdIos Apr 23, 2026
0897294
Apply suggestions from code review
dgarijo Apr 23, 2026
6b4d7d6
Merge pull request #967 from juanjemdIos/master
dgarijo Apr 23, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
3 changes: 2 additions & 1 deletion README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -27,6 +27,7 @@ Given a readme file (or a GitHub/Gitlab repository) SOMEF will extract the follo
- **Build file**: Build file(s) of the project. For example, files used to create a Docker image for the target software, package files, etc.
- **Citation**: Preferred citation(s) as the authors have stated in their readme file. SOMEF recognizes Bibtex, Citation File Format files and other means by which authors cite their papers (e.g., by in-text citation).
For CITATION.cff files, SOMEF now generates two separate entries: one for the software tool and another for the preferred citation (if available). This ensures metadata like DOI or version is correctly assigned to each entity.
SOMEF now performs citation reconciliation: scholarly publications (articles) are assigned in codemeta to `referencePublication`, while the software itself is credited in `creditText`. (See https://somef.readthedocs.io/en/latest/output/#codemeta-format).
We recognize the following properties:
- Title: Title of the publication
- Author: list of author names in the publication
Expand All @@ -41,7 +42,7 @@ We recognize the following properties:
- **Contact**: Contact person responsible for maintaining a software component
- **Continuous integration**: Link to continuous integration service(s)
- **Contribution guidelines**: Text indicating how to contribute to this code repository
- **Contributors**: Contributors to a software component. Note: Contributor metadata is exported from metadata files (e.g., CodeMeta, CONTRIBUTORS, etc.) not from git logs.
- **Contributor**: Contributors to a software component. Note: Contributor metadata is exported from metadata files (e.g., CodeMeta, CONTRIBUTORS, etc.) not from git logs.
- **Creation date**: Date when the repository was created
- **Copyright holder**: Entity or individual owning the rights to the software. The year is also extracted, if available.
- **Date updated**: Date of last release.
Expand Down
10 changes: 5 additions & 5 deletions docs/author.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,11 @@ These fields are defined in the [Authors file specification](https://opensource.

| Software metadata category | SOMEF metadata JSON path | AUTHORS metadata file field |
|-------------------------------|---------------------------------------------|------------------------------|
| authors - value | authors[i].result.value | *(1)* value |
| authors - name | authors[i].result.name | *(2)* name |
| authors - email | authors[i].result.email | *(3)* email |
| authors - given name | authors[i].result.given_name | *(4)* if type person |
| authors - last name | authors[i].result.last_name | *(5)* if type person |
| author - value | author[i].result.value | *(1)* value |
| author - name | author[i].result.name | *(2)* name |
| author - email | author[i].result.email | *(3)* email |
| author - given name | author[i].result.given_name | *(4)* if type person |
| author - last name | author[i].result.last_name | *(5)* if type person |

---

Expand Down
2 changes: 1 addition & 1 deletion docs/bower.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ These fields are defined in the [Bower specification](https://github.com/bower/s

| Software metadata category | SOMEF metadata JSON path | BOWER.JSON metadata file field |
|-----------------------------|---------------------------------------|---------------------|
| authors | authors[i].result.value | authors[] |
| author | author[i].result.value | authors[] |
| description | description[i].result.value | description |
| has_package_file | has_package_file[i].result.value | URL of the bower.json file |
| homepage | homepage[i].result.value | homepage |
Expand Down
6 changes: 3 additions & 3 deletions docs/cargo.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,9 +3,9 @@ These fields are defined in the [Cargo.toml specification](https://doc.rust-lang

| Software metadata category | SOMEF metadata JSON path | CARGO.TOML metadata file field |
|-------------------------------|--------------------------------------------|------------------------------|
| authors - value | authors[i].result.value | package.authors |
| authors - name | authors[i].result.name | package.authors *(1)* |
| authors - email | authors[i].result.email | package.authors *(2)* |
| author - value | author[i].result.value | package.authors |
| author - name | author[i].result.name | package.authors *(1)* |
| author - email | author[i].result.email | package.authors *(2)* |
| code_repository | code_repository[i].result.value | package.repository |
| description | description[i].result.value | package.description |
| has_package_file | has_package_file[i].result.value | URL of the cargo.toml file |
Expand Down
8 changes: 4 additions & 4 deletions docs/citationcff.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,10 @@ These fields are defined in the [CITATION.cff specification](https://citation-fi

| Software metadata category | SOMEF metadata JSON path | CITATION.cff metadata file field |
|----------------------------|---------------------------------------|---------------------|
| citation - authors - name | citation[i].result.authors[j].name | authors / preferred-citation.authors |
| citation - authors - family_name | citation[i].result.authors[j].family_name | authors.family-names |
| citation - authors - given_name | citation[i].result.authors[j].given_name | authors.given-names |
| citation - authors - url | citation[i].result.authors[j].url | authors.orcid |
| citation - author - name | citation[i].result.author[j].name | authors / preferred-citation.authors |
| citation - author - family_name | citation[i].result.author[j].family_name | authors.family-names |
| citation - author - given_name | citation[i].result.author[j].given_name | authors.given-names |
| citation - author - url | citation[i].result.author[j].url | authors.orcid |
| citation - doi | citation[i].result.doi | doi / preferred-citation.doi |
| citation - datePublished | citation[i].result.datePublished | date-released |
| citation - is_preferred_citation | citation[i].result.is_preferred_citation | "True" if from preferred-citation. Omitted otherwise|
Expand Down
20 changes: 10 additions & 10 deletions docs/codemetajson.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -4,23 +4,23 @@ These fields are defined in the [Codemeta specification](https://github.com/code
| Software metadata category | SOMEF metadata JSON path | CODEMETA.JSON metadata file field |
|-------------------------------|------------------------------|--------------------------------------------|
| application_domain | application_domain[i].result.value | applicationCategory |
| authors - value | authors[i].result.value | author.name or author.givenName + author.familyName |
| authors - email | authors[i].result.email | author.email |
| authors - affiliation | authors[i].result.affiliation | author.affiliation |
| authors - identifier | authors[i].result.identifier | author.identifier or author.@id |
| author - value | author[i].result.value | author.name or author.givenName + author.familyName |
| author - email | author[i].result.email | author.email |
| author - affiliation | author[i].result.affiliation | author.affiliation |
| author - identifier | author[i].result.identifier | author.identifier or author.@id |
| citation - value | citation[i].result.value | referencePublication.name or referencePublication.title |
| citation - title | citation[i].result.title | referencePublication.name or referencePublication.title |
| citation - url | citation[i].result.url | referencePublication.url |
| citation - date published | citation[i].result.date_published | referencePublication.datePublished
| citation - doi | citation[i].result.doi | referencePublication.identifier |
| code_repository | code_repository[i].result.value | codeRepository |
| continuous_integration | continuous_integration[i].result.value | contIntegration |
| contributors - value | contributors[i].result.value | contributor.givenName + contributor.familyName or just name if organization |
| contributors - name | contributors[i].result.value | contributor.givenName + contributor.familyName or just name if organization |
| contributors - last_name | contributors[i].result.value | contributor.familyName |
| contributors - given_name | contributors[i].result.value | contributor.givenName |
| contributors - identifier | contributors[i].result.value | contributor.@id |
| contributors - email | contributors[i].result.value | contributor.email |
| contributor - value | contributor[i].result.value | contributor.givenName + contributor.familyName or just name if organization |
| contributor - name | contributor[i].result.value | contributor.givenName + contributor.familyName or just name if organization |
| contributor - last_name | contributor[i].result.value | contributor.familyName |
| contributor - given_name | contributor[i].result.value | contributor.givenName |
| contributor - identifier | contributor[i].result.value | contributor.@id |
| contributor - email | contributor[i].result.value | contributor.email |
| date_created | date_created[i].result.value | dateCreated |
| date_updated | date_updated[i].result.value | dateModified |
| date_published | date_published[i].result .value | datePublished |
Expand Down
10 changes: 5 additions & 5 deletions docs/composer.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,11 +3,11 @@ These fields are defined in the [Composer.json specification](https://getcompose

| Software metadata category | SOMEF metadata JSON path | COMPOSER.JSON metadata file field |
|-------------------------------|-----------------------------------|-----------------------------------|
| authors - value | authors[i].result.value | authors.name |
| authors - name | authors[i].result.name | authors.name |
| authors - name | authors[i].result email | authors.email |
| authors - url | authors[i].result.url | authors.homepage |
| authors - role | authors[i].result.role | authors.role |
| author - value | author[i].result.value | authors.name |
| author - name | author[i].result.name | authors.name |
| author - name | author[i].result email | authors.email |
| author - url | author[i].result.url | authors.homepage |
| author - role | author[i].result.role | authors.role |
| code_repository | code_repository[i].result.value | repository or repository.url |
| description | description[i].result.value | description |
| has_package_file | has_package_file[i].result.value | URL of the composer.json file |
Expand Down
4 changes: 2 additions & 2 deletions docs/description.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@ These fields are defined in the [DESCRIPTON specification](https://r-pkgs.org/de

| Software metadata category | SOMEF metadata JSON path | DESCRIPTION metadata file field |
|-------------------------------|---------------------------------|---------------------|
| authors | authors[i].result.value | Authors *(1)* |
| authors | authors[i].result.email | Authors *(2)* |
| author | authors[i].result.value | Authors *(1)* |
| author | authors[i].result.email | Authors *(2)* |
| code_repository | code_repository[i].result.value | URL *(3)* |
| description | description[i].result.value | Description *(4)* |
| has_package_file | has_package_file[i].result.value | URL of the DESCRIPTION file |
Expand Down
4 changes: 2 additions & 2 deletions docs/dockerfiledoc.md → docs/docker_file_doc.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -6,8 +6,8 @@ according to the OCI Image Specification, following the

| Software metadata category | SOMEF metadata JSON path | DOCKERFILE metadata file field |
|-----------------------------|-----------------------------------------|------------------------------------|
| authors | authors[i].result.value | org.opencontainers.image.authors *(1)* |
| authors | authors[i].result.value | LABEL maintainer *(1)* |
| author | author[i].result.value | org.opencontainers.image.authors *(1)* |
| author | author[i].result.value | LABEL maintainer *(1)* |
| code_repository | code_repository[i].result.value | org.opencontainers.image.url |
| description | description[i].result.value | org.opencontainers.image.description |
| documentation | documentation[i].result.value | org.opencontainers.image.documentation |
Expand Down
2 changes: 1 addition & 1 deletion docs/gemspec.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@ These fields are defined in the [Ruby Gems specification](https://guides.rubygem

| Software metadata category | SOMEF metadata JSON path | .gemspec metadata file field |
|-------------------------------|--------------------------------|--------------------------------------|
| authors | authors[i].result.value | gem.authors *(1)* |
| author | authors[i].result.value | gem.authors *(1)* |
| description | description[i].resultvalue | description *(2)* |
| has_package_file | has_package_file[i].result.value | URL of the filename.gemspec file |
| homepage | homepage[i].result.value | homepage *(3)* |
Expand Down
5 changes: 3 additions & 2 deletions docs/index.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,7 @@ Given a readme file (or a GitHub repository) SOMEF will extract the following ca
- encoding_format: format of the file
- upload_date: date of publishing
- download_count: numbers of downloads
- **Authors**: Person(s) or organization(s) responsible for the project. We recognize the following properties:
- **Author**: Person(s) or organization(s) responsible for the project. We recognize the following properties:
- Name: name of the author (including last name)
- Given name: First name of an author
- Family name: Last name of an author
Expand All @@ -34,6 +34,7 @@ Given a readme file (or a GitHub repository) SOMEF will extract the following ca
- **Build file**: Build file(s) of the project. For example, files used to create a Docker image for the target software, package files, etc.
- **Citation**: Preferred citation(s) as the authors have stated in their readme file. SOMEF recognizes Bibtex, Citation File Format files and other means by which authors cite their papers (e.g., by in-text citation).
For CITATION.cff files, SOMEF now generates two separate entries: one for the software tool and another for the preferred citation (if available). This ensures metadata like DOI or version is correctly assigned to each entity.
SOMEF now performs citation reconciliation: scholarly publications (articles) are assigned in codemeta to `referencePublication`, while the software itself is credited in `creditText`. (See https://somef.readthedocs.io/en/latest/output/#codemeta-format).
We recognize the following properties:
- Title: Title of the publication
- Author: list of author names in the publication
Expand All @@ -49,7 +50,7 @@ We recognize the following properties:
- **Contact**: Contact person responsible for maintaining a software component
- **Continuous integration**: Link to continuous integration service(s)
- **Contribution guidelines**: Text indicating how to contribute to this code repository
- **Contributors**: Contributors to a software component. Note: Contributor metadata is exported from metadata files (e.g., CodeMeta, CONTRIBUTORS, etc.) not from git logs.
- **Contributor**: Contributors to a software component. Note: Contributor metadata is exported from metadata files (e.g., CodeMeta, CONTRIBUTORS, etc.) not from git logs.
- **Copyright holder**: Entity or individual owning the rights to the software. The year is also extracted, if available.
- **Creation date**: Date when the repository was created
- **Date updated**: Date of last release.
Expand Down
4 changes: 2 additions & 2 deletions docs/julia.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -3,8 +3,8 @@ These fields are defined in the [Julia projects specification](https://docs.juli

| Software metadata category | SOMEF metadata JSON path | julia pyproject.toml metadata file field |
|-------------------------------|--------------------------------|---------------------------------------------------|
| authors - name | authors[i].result.name | authors *(1)* |
| authors - email | authors[i].result.email | authors *(1)* |
| author - name | author[i].result.name | authors *(1)* |
| author - email | author[i].result.email | authors *(1)* |
| package_id | package_id[i].result.value | name |
| has_package_file | has_package_file[i].result.value | URL of the Project.toml file |
| identifier | identifier[i].result .value | uuid |
Expand Down
Loading
Loading