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new properties (license, version) from citation.cff. Fixes #935 #948

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dgarijo merged 20 commits into from
Apr 16, 2026
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new properties (license, version) from citation.cff. Fixes #935 #948

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bb1845a
new properties (license, version) from citation.cff. Fixes #935
juanjemdIos Apr 7, 2026
f76adad
Improve extraction and structure of citation and reference publications
juanjemdIos Apr 10, 2026
da0c518
Revert reference_publication category to keep all citations in CAT_CI…
juanjemdIos Apr 10, 2026
d23cae9
upperCase typo error writting "Widoco" in a test
juanjemdIos Apr 10, 2026
78055b1
Standardize license fields and consolidate results. Fixes #955
juanjemdIos Apr 13, 2026
3d84e8f
fix documentation consistency and order tables. Fixes #954
juanjemdIos Apr 14, 2026
4ddc072
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dgarijo Apr 14, 2026
c9e0564
Update docs/index.md
juanjemdIos Apr 14, 2026
5686a9e
Update docs/index.md
juanjemdIos Apr 14, 2026
cce43bf
Update docs/index.md
juanjemdIos Apr 14, 2026
c5a74c5
resolve category inconsistencies and standardize properties and types…
juanjemdIos Apr 15, 2026
ef50754
Merge branch 'master' of https://github.com/juanjemdIos/somef
juanjemdIos Apr 15, 2026
20e1ef0
Funding and funder in codemeta export. Fixes #960
juanjemdIos Apr 15, 2026
b5e04da
Fixes mkdocs and ensures file names. CSS. New citation.cff and bibtex…
juanjemdIos Apr 16, 2026
5e46dfb
update supported dependency types in output.md
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10 changes: 8 additions & 2 deletions README.md
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Expand Up @@ -24,12 +24,18 @@ Given a readme file (or a GitHub/Gitlab repository) SOMEF will extract the follo
- Email: email of author
- URL: website or ORCID associated with the author
- **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 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). We aim to recognize the following properties:
- **Citation**: Preferred citation 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).
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For CITATION.cff files, SOMEF now generates two separate entries: one for the software (is_preferred_citation: False) and another for the preferred citation (is_preferred_citation: True). This ensures metadata like DOI or version is correctly assigned to each entity.
We aim to recognize the following properties:
- Title: Title of the publication
- Author: list of author names in the publication
- URL: URL of the publication
- DOI: Digital object identifier of the publication
- Date published
- Version: Software version (if applicable)
- Journal: Journal name where the paper was published
- Year: Year of publication
- Pages: Page range in the journal
- **Code of conduct**: Link to the code of conduct of the project
- **Code repository**: Link to the GitHub/GitLab repository used for the extraction
- **Contact**: Contact person responsible for maintaining a software component
Expand All @@ -54,7 +60,7 @@ Given a readme file (or a GitHub/Gitlab repository) SOMEF will extract the follo
- **Invocation**: Execution command(s) needed to run a scientific software component
- **Issue tracker**: Link where to open issues for the target repository
- **Keywords**: set of terms used to commonly identify a software component
- **License**: License and usage terms of a software component
- **License**: License and usage terms of a software component. Now we also extract license from citation.cff.
- **Logo**: Main logo used to represent the target software component
- **Maintainer**: Individuals or teams responsible for maintaining the software component, extracted from the CODEOWNERS file
- **Name**: Name identifying a software component
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12 changes: 9 additions & 3 deletions docs/index.md
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Expand Up @@ -31,12 +31,18 @@ Given a readme file (or a GitHub repository) SOMEF will extract the following ca
- URL: website or ORCID associated with the author
- Affiliation: name of organization or affiliation
- **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 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). We aim to recognize the following properties:
- **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 (is_preferred_citation: False) and another for the preferred citation (is_preferred_citation: True). This ensures metadata like DOI or version is correctly assigned to each entity.
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but if there is no preferred citation, then the software one is not false.
Instead of generating False, I would only leave is_preferred_citaiton: True when we find prefered citation. And do not add anything otherwise.

We aim to recognize the following properties:
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- Title: Title of the publication
- Author: list of author names in the publication
- URL: URL of the publication
- DOI: Digital object identifier of the publication
- Date published:
- Date published
- Version: Software version (if applicable)
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- Journal: Journal name where the paper was published
- Year: Year of publication
- Pages: Page range in the journal
- **Code of conduct**: Link to the code of conduct of the project
- **Code repository**: Link to the GitHub/GitLab repository used for the extraction
- **Contact**: Contact person responsible for maintaining a software component
Expand All @@ -62,7 +68,7 @@ Given a readme file (or a GitHub repository) SOMEF will extract the following ca
- **Invocation**: Execution command(s) needed to run a scientific software component
- **Issue tracker**: Link where to open issues for the target repository
- **Keywords**: set of terms used to commonly identify a software component
- **License**: License and usage terms of a software component
- **License**: License and usage terms of a software component. Now we also extract license from citation.cff.
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- **Logo**: Main logo used to represent the target software component
- **Name**: Name identifying a software component
- **Ontologies**: URL and path to the ontology files present in the repository
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68 changes: 38 additions & 30 deletions docs/output.md
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Expand Up @@ -68,7 +68,7 @@ SOMEF aims to recognize the following categories (in alphabetical order):
- `acknowledgement`: Any text that the authors have prepared to acknnowledge the contribution from others, or project funding.
- `application_domain`: The application domain of the repository. This may be related to the research area of a software component (e.g., Astrophysics) or the general domain/functionality of the tool (i.e., machine learning projects). See all current recognized application domains [here](https://somef.readthedocs.io/en/latest/#myfootnote1).
- `authors`: Person or organization responsible of the project. This property is also used to indicate the responsible entities of a publication associated with the code repository.
- `citation`: Software citation (usually in `.bib` form) as the authors have stated in their readme file, or through a `CFF` file.
- `citation`: Software citation (usually in .bib or .cff format). SOMEF extracts and structures the metadata from these files (including authors, titles, and DOIs) instead of just returning a raw string.
- `code_of_conduct`: Link to the code of conduct file of the project
- `code_repository`: Link to the source code (typically the repository where the readme can be found)
- `contact`: Contact person responsible for maintaining a software component.
Expand All @@ -88,7 +88,9 @@ SOMEF aims to recognize the following categories (in alphabetical order):
- `forks_url`: Links to forks made of the project (GitHub only)
- `full_name`: Name + owner (owner/name) (if available)
- `full_title`: If the repository has a short name, we will attempt to extract the longer version of the repository name. For example, a repository may be called "Widoco", but the longer title is "Wizard for documenting ontologies".
- `funding`: Funding code for the related project.
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wait, we don't do this

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Please double check

- `has_build_file`: Build file to create a Docker image for the target software
- `has_package_file`: Specifies what package file is present in the code repository.
- `has_script_file`: Snippets of code contained in the repository.
- `homepage`: URL of the item.
- `identifier`: Identifiers detected within a repository (e.g., Digital Object Identifier).
Expand All @@ -105,8 +107,10 @@ SOMEF aims to recognize the following categories (in alphabetical order):
- `owner`: Name of the user or organization in charge of the repository
- `package_distribution`: Link to official package repositories where the software can be downloaded from (e.g., `pypi`).
- `package_file`: Link to a package file used in the repository (e.g., `pyproject.toml`, `setup.py`).
- `package_id`: Identifier extracted from packages. (e.g., `packages.json`)
- `programming_languages`: Languages used in the repository.
- `readme_url`: URL to the main README file in the repository.
- `reference_publication`: URL to the paper associated with the code repository.
- `related_papers`: URL to possible related papers within the repository stated within the readme file.
- `releases`: Pointer to the available versions of a software component.
- `repository_status`: Repository status as it is described in [repostatus.org](https://www.repostatus.org/).
Expand All @@ -118,11 +122,7 @@ SOMEF aims to recognize the following categories (in alphabetical order):
- `type`: Software type: Commandline Application, Notebook Application, Ontology, Scientific Workflow. Non-Software types: Static Website, Uncategorized
- `usage`: Usage examples and considerations of a code repository.
- `workflows`: URL and path to the computational workflow files present in the repository.
- `homepage`: URL to the homepage of the software or organization.
- `reference_publication`: URL to the paper associated with the code repository.
- `package_id`: Identifier extracted from packages. (e.g., `packages.json`)
- `funding`: Funding code for the related project.
- `has_package_file`: Specifies what package file is present in the code repository.


The following table summarized the properties used to describe a `category`:

Expand Down Expand Up @@ -211,22 +211,24 @@ The table below summarizes all types and their corresponding properties:
| **zipball_url** | Release | Url | URL to the zip file where to download a software release | -->


The tables below summarizes all types and their corresponding properties-
The tables below summarizes all types and their corresponding properties.
The following object types are currently supported (aligned with Schema.org and CodeMeta vocabularies)

An AGENT has the following properties:
An Agent has the following properties:

| Property | Expected value | Definition |
|---|---|---|
| **affiliation** | String | name of organization or affiliation |
| **email** | String | Email of an author |
| **family_name** | String | Last name of an author |
| **given_name** | String | First name of an author |
| **identifier** | String | id of an agent |
| **name** | String | Name used to designate the person or organization|
| **role** | String | The role of the agent in the development or maintenance of this software component |
| **url** | Url | Uniform resource locator of the resource |
| **affiliation** | String | name of organization or affiliation |
| **identifier** | String | id of an agent |
| **role** | String | role of agent |

An ASSET has the following properties:

An Asset has the following properties:

| Property | Expected value | Definition |
|---|---|---|
Expand All @@ -239,25 +241,25 @@ An ASSET has the following properties:
| **url** | Url | Uniform resource locator of the resource |



A LICENSE has the following properties:
A License has the following properties:

| Property | Expected value | Definition |
|---|---|---|
| **identifier** | String | id of licence |
| **name** | String | Title or name of the license |
| **spdx_id** | String | Spdx id corresponding to this license |
| **url** | Url | Uniform resource locator of the license |
| **identifier** | String | id of licence |

A PROGRAMMING_LANGUAGE has the following properties:

A Programming_language has the following properties:

| Property | Expected value | Definition |
|---|---|---|
| **name** | String | Name of the language |
| **size** | Integer | File size content (bytes) of a code repository using a given programming language |


A PUBLICATION has the following properties:
A Publication has the following properties:

| Property | Expected value | Definition |
|---|---|---|
Expand All @@ -267,7 +269,7 @@ A PUBLICATION has the following properties:
| **url** | Url | Uniform resource locator of the resource |


A RELEASE has the following properties:
A Release has the following properties:

| Property | Expected value | Definition |
|---|---|---|
Expand All @@ -285,45 +287,51 @@ A RELEASE has the following properties:
| **zipball_url** | Url | URL to the zip file where to download a software release |


A REQUIREMENT has the following properties:
A Requirement has the following properties:

| Property | Expected value | Definition |
|---|---|---|
| **name** | String | Name of the requeriment |
| **version** | String | named version of a requeriment |
| **dependency_type** | String | type: dev, runtime... Indicates whether the dependency is required at runtime or only for development/testing |
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List all dependency types we support.
We support 3: development, runtime and documentation

| **dependency_resolver** | String | Identifies the ecosystem or package manager that resolves the dependency (e.g., npm, bower, pip, python, poetry, pdm, cargo, julia, maven, publicode).|
| **name** | String | Name of the requeriment |
| **version** | String | named version of a requeriment |

A RUNTIME_PLATFORM has the following properties:

A Runtime_platform has the following properties:

| Property | Expected value | Definition |
|---|---|---|
| **name** | String | Name of the runtime platform (e.g., Java) |
**version** | String | version of the runtime platform |
| **value** | String | name and version of the runtime platform |
| **version** | String | version of the runtime platform |


A SCHOLARLY_ARTICLE has the following properties:
A Scholarly_article has the following properties:

| Property | Expected value | Definition |
|---|---|---|
| **authors** | List of Agent| List of authors responsible for the publication, providing structured metadata for each |
| **date_published** | String | Date when the article or citation was officially published. |
| **doi** | String | Digital Object Identifier (DOI) of the reference, usually returned as a full URL.|
| **journal** | String | Journal where the publication appeared |
| **pages** | String | Page range of the publication |
| **title** | String | Title of reference or citation |
| **value** | String | Title of reference or citation |
| **url** | String | Link to reference or citation |
| **date_published** | String | date of publication reference or citation |
| **doi** | String | Identifier of reference|
| **value** | String | Title of reference or citation |
| **year** | Number | Year of publication |


A SOFTWARE_APPLICATION has the following properties:
A Software_application has the following properties:
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This one does not make a lot of sense. What is the difference between this and Requirement?


| Property | Expected value | Definition |
|---|---|---|
| **development_type** | String | runtime or dev |
| **name** | String | Name of the software |
| **value** | String | Name and version of the software |
| **version** | String | version of software |
| **development_type** | String | runtime or dev |

A TEXT_EXCERPT has the following properties:

A Text_excerpt has the following properties:

| Property | Expected value | Definition |
|---|---|---|
Expand Down
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