From a7d9d6c545e871a1f495a69f0b64fbc63b06fac2 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Thu, 16 Jun 2022 16:27:39 -0700 Subject: [PATCH 1/6] add auto generated citation --- CITATION.cff | 102 +++++++++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 102 insertions(+) create mode 100644 CITATION.cff diff --git a/CITATION.cff b/CITATION.cff new file mode 100644 index 00000000..8ed81001 --- /dev/null +++ b/CITATION.cff @@ -0,0 +1,102 @@ +cff-version: '1.1.0' +message: 'Please cite the following works when using this software.' +abstract: "Abstract\n Despite progress in the development of standards for describing and exchanging scientific information, the lack of easy-to-use standards for mapping between different representations of the same or similar objects in different databases poses a major impediment to data integration and interoperability. Mappings often lack the metadata needed to be correctly interpreted and applied. For example, are two terms equivalent or merely related? Are they narrow or broad matches? Or are they associated in some other way? Such relationships between the mapped terms are often not documented, which leads to incorrect assumptions and makes them hard to use in scenarios that require a high degree of precision (such as diagnostics or risk prediction). Furthermore, the lack of descriptions of how mappings were done makes it hard to combine and reconcile mappings, particularly curated and automated ones. We have developed the Simple Standard for Sharing Ontological Mappings (SSSOM) which addresses these problems by: (i) Introducing a machine-readable and extensible vocabulary to describe metadata that makes imprecision, inaccuracy and incompleteness in mappings explicit. (ii) Defining an easy-to-use simple table-based format that can be integrated into existing data science pipelines without the need to parse or query ontologies, and that integrates seamlessly with Linked Data principles. (iii) Implementing open and community-driven collaborative workflows that are designed to evolve the standard continuously to address changing requirements and mapping practices. (iv) Providing reference tools and software libraries for working with the standard. In this paper, we present the SSSOM standard, describe several use cases in detail and survey some of the existing work on standardizing the exchange of mappings, with the goal of making mappings Findable, Accessible, Interoperable and Reusable (FAIR). The SSSOM specification can be found at http://w3id.org/sssom/spec.\n Database URL: http://w3id.org/sssom/spec" +authors: + - family-names: 'Matentzoglu' + given-names: 'Nicolas' + - family-names: 'Balhoff' + given-names: 'James P' + - family-names: 'Bello' + given-names: 'Susan M' + - family-names: 'Bizon' + given-names: 'Chris' + - family-names: 'Brush' + given-names: 'Matthew' + - family-names: 'Callahan' + given-names: 'Tiffany J' + - family-names: 'Chute' + given-names: 'Christopher G' + - family-names: 'Duncan' + given-names: 'William D' + - family-names: 'Evelo' + given-names: 'Chris T' + - family-names: 'Gabriel' + given-names: 'Davera' + - family-names: 'Graybeal' + given-names: 'John' + - family-names: 'Gray' + given-names: 'Alasdair' + - family-names: 'Gyori' + given-names: 'Benjamin M' + - family-names: 'Haendel' + given-names: 'Melissa' + - family-names: 'Harmse' + given-names: 'Henriette' + - family-names: 'Harris' + given-names: 'Nomi L' + - family-names: 'Harrow' + given-names: 'Ian' + - family-names: 'Hegde' + given-names: 'Harshad B' + - family-names: 'Hoyt' + given-names: 'Amelia L' + - family-names: 'Hoyt' + given-names: 'Charles T' + - family-names: 'Jiao' + given-names: 'Dazhi' + - family-names: 'Jiménez-Ruiz' + given-names: 'Ernesto' + - family-names: 'Jupp' + given-names: 'Simon' + - family-names: 'Kim' + given-names: 'Hyeongsik' + - family-names: 'Koehler' + given-names: 'Sebastian' + - family-names: 'Liener' + given-names: 'Thomas' + - family-names: 'Long' + given-names: 'Qinqin' + - family-names: 'Malone' + given-names: 'James' + - family-names: 'McLaughlin' + given-names: 'James A' + - family-names: 'McMurry' + given-names: 'Julie A' + - family-names: 'Moxon' + given-names: 'Sierra' + - family-names: 'Munoz-Torres' + given-names: 'Monica C' + - family-names: 'Osumi-Sutherland' + given-names: 'David' + - family-names: 'Overton' + given-names: 'James A' + - family-names: 'Peters' + given-names: 'Bjoern' + - family-names: 'Putman' + given-names: 'Tim' + - family-names: 'Queralt-Rosinach' + given-names: 'Núria' + - family-names: 'Shefchek' + given-names: 'Kent' + - family-names: 'Solbrig' + given-names: 'Harold' + - family-names: 'Thessen' + given-names: 'Anne' + - family-names: 'Tudorache' + given-names: 'Tania' + - family-names: 'Vasilevsky' + given-names: 'Nicole' + - family-names: 'Wagner' + given-names: 'Alex H' + - family-names: 'Mungall' + given-names: 'Christopher J' +doi: '10.1093/database/baac035' +identifiers: + - type: 'doi' + value: '10.1093/database/baac035' + - type: 'url' + value: 'http://dx.doi.org/10.1093/database/baac035' + - type: 'other' + value: 'urn:issn:1758-0463' +title: 'A Simple Standard for Sharing Ontological Mappings (SSSOM)' +url: 'http://dx.doi.org/10.1093/database/baac035' From e1d9c57aa2f118a28d459cd5af37f0b9c5f51a00 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Thu, 16 Jun 2022 16:29:14 -0700 Subject: [PATCH 2/6] update changelog --- CHANGELOG.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6b7da9d4..e37a39ee 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,8 +1,10 @@ # Changelog for SSSOM +## SSSOM version 1.1 +- added citation.cff file ## SSSOM version 1.0 - Changed `match_type` logic to `mapping_justification` ([issue](https://github.com/mapping-commons/sssom/issues/150)). ## SSSOM version 0.9 - Initial release -- see https://github.com/mapping-commons/sssom/releases/tag/0.9.0 \ No newline at end of file +- see https://github.com/mapping-commons/sssom/releases/tag/0.9.0 From 7c07aa7cee88aaac62d04a145bfc97e647f512db Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Fri, 15 Jul 2022 08:20:12 -0700 Subject: [PATCH 3/6] superfences interferes with mermaid, removing to allow diagrams to be generated correctly --- mkdocs.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/mkdocs.yml b/mkdocs.yml index b5d2006f..a2bd1a1c 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -14,7 +14,6 @@ markdown_extensions: - pymdownx.highlight: - pymdownx.inlinehilite - pymdownx.snippets - - pymdownx.superfences - pymdownx.tabbed: - pymdownx.critic - pymdownx.caret From f0ecaf768309a3017e2d774434d26924a68d6923 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Fri, 15 Jul 2022 08:22:12 -0700 Subject: [PATCH 4/6] remove changelog addition --- CHANGELOG.md | 2 -- 1 file changed, 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index fc622a33..6ab25bce 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,4 @@ # Changelog for SSSOM -## SSSOM version 1.1 -- added citation.cff file ## SSSOM version 1.0 From b1ebb20c051a3033b1ede3d03a0dec6c90543458 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Fri, 15 Jul 2022 08:50:22 -0700 Subject: [PATCH 5/6] add mermaid2 plugin --- mkdocs.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/mkdocs.yml b/mkdocs.yml index a2bd1a1c..63cfe2b7 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -10,6 +10,7 @@ theme: - content.tabs.link plugins: - search + - mermaid2 markdown_extensions: - pymdownx.highlight: - pymdownx.inlinehilite From 49dba64be41889e9de0baaf904b9b221fc73a003 Mon Sep 17 00:00:00 2001 From: Sierra Taylor Moxon Date: Fri, 15 Jul 2022 09:14:36 -0700 Subject: [PATCH 6/6] update dependencies --- poetry.lock | 399 +++++++++++++++++++++++++++---------------------- pyproject.toml | 7 +- 2 files changed, 226 insertions(+), 180 deletions(-) diff --git a/poetry.lock b/poetry.lock index 76d55f44..d35b46a6 100644 --- a/poetry.lock +++ b/poetry.lock @@ -38,7 +38,7 @@ tests_no_zope = ["coverage[toml] (>=5.0.2)", "hypothesis", "pympler", "pytest (> [[package]] name = "babel" -version = "2.10.1" +version = "2.10.3" description = "Internationalization utilities" category = "dev" optional = false @@ -47,9 +47,24 @@ python-versions = ">=3.6" [package.dependencies] pytz = ">=2015.7" +[[package]] +name = "beautifulsoup4" +version = "4.11.1" +description = "Screen-scraping library" +category = "main" +optional = false +python-versions = ">=3.6.0" + +[package.dependencies] +soupsieve = ">1.2" + +[package.extras] +html5lib = ["html5lib"] +lxml = ["lxml"] + [[package]] name = "certifi" -version = "2022.5.18.1" +version = "2022.6.15" description = "Python package for providing Mozilla's CA Bundle." category = "main" optional = false @@ -68,19 +83,19 @@ rdflib = ">=0.4.2" [[package]] name = "chardet" -version = "4.0.0" -description = "Universal encoding detector for Python 2 and 3" +version = "5.0.0" +description = "Universal encoding detector for Python 3" category = "dev" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +python-versions = ">=3.6" [[package]] name = "charset-normalizer" -version = "2.0.12" +version = "2.1.0" description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet." category = "main" optional = false -python-versions = ">=3.5.0" +python-versions = ">=3.6.0" [package.extras] unicode_backport = ["unicodedata2"] @@ -99,7 +114,7 @@ importlib-metadata = {version = "*", markers = "python_version < \"3.8\""} [[package]] name = "colorama" -version = "0.4.4" +version = "0.4.5" description = "Cross-platform colored terminal text." category = "main" optional = false @@ -135,6 +150,14 @@ category = "dev" optional = false python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*" +[[package]] +name = "editorconfig" +version = "0.12.3" +description = "EditorConfig File Locator and Interpreter for Python" +category = "main" +optional = false +python-versions = "*" + [[package]] name = "et-xmlfile" version = "1.1.0" @@ -147,7 +170,7 @@ python-versions = ">=3.6" name = "ghp-import" version = "2.1.0" description = "Copy your docs directly to the gh-pages branch." -category = "dev" +category = "main" optional = false python-versions = "*" @@ -199,7 +222,7 @@ python-versions = ">=3.5" [[package]] name = "imagesize" -version = "1.3.0" +version = "1.4.1" description = "Getting image size from png/jpeg/jpeg2000/gif file" category = "dev" optional = false @@ -207,7 +230,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "importlib-metadata" -version = "4.11.4" +version = "4.12.0" description = "Read metadata from Python packages" category = "main" optional = false @@ -220,11 +243,11 @@ zipp = ">=0.5" [package.extras] docs = ["sphinx", "jaraco.packaging (>=9)", "rst.linker (>=1.9)"] perf = ["ipython"] -testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.0.1)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"] +testing = ["pytest (>=6)", "pytest-checkdocs (>=2.4)", "pytest-flake8", "pytest-cov", "pytest-enabler (>=1.3)", "packaging", "pyfakefs", "flufl.flake8", "pytest-perf (>=0.9.2)", "pytest-black (>=0.3.7)", "pytest-mypy (>=0.9.1)", "importlib-resources (>=1.3)"] [[package]] name = "importlib-resources" -version = "5.7.1" +version = "5.8.0" description = "Read resources from Python packages" category = "main" optional = false @@ -252,7 +275,7 @@ six = "*" name = "jinja2" version = "3.1.2" description = "A very fast and expressive template engine." -category = "dev" +category = "main" optional = false python-versions = ">=3.7" @@ -262,6 +285,18 @@ MarkupSafe = ">=2.0" [package.extras] i18n = ["Babel (>=2.7)"] +[[package]] +name = "jsbeautifier" +version = "1.14.4" +description = "JavaScript unobfuscator and beautifier." +category = "main" +optional = false +python-versions = "*" + +[package.dependencies] +editorconfig = ">=0.12.2" +six = ">=1.13.0" + [[package]] name = "json-flattener" version = "0.1.9" @@ -330,7 +365,7 @@ python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*" [[package]] name = "jsonschema" -version = "4.6.0" +version = "4.7.2" description = "An implementation of JSON Schema validation for Python" category = "main" optional = false @@ -349,7 +384,7 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339- [[package]] name = "linkml" -version = "1.2.13" +version = "1.3.0" description = "Linked Open Data Modeling Language" category = "dev" optional = false @@ -366,7 +401,7 @@ jinja2 = "*" jsonasobj2 = ">=1.0.3,<2.0.0" jsonschema = ">=3.0.1" linkml-dataops = "*" -linkml-runtime = "1.2.16" +linkml-runtime = ">=1.3.0,<2.0.0" myst-parser = "*" openpyxl = "*" parse = "*" @@ -403,7 +438,7 @@ linkml-runtime = ">=1.1.6" [[package]] name = "linkml-runtime" -version = "1.2.16" +version = "1.3.0" description = "Runtime environment for LinkML, the Linked open data modeling language" category = "main" optional = false @@ -416,18 +451,18 @@ hbreader = "*" json-flattener = ">=0.1.9" jsonasobj2 = ">=1.0.4,<2.0.0" jsonschema = ">=3.2.0" -prefixcommons = "*" +prefixcommons = "0.1.11" pyyaml = "*" rdflib = ">=6.0.0" requests = "*" [[package]] name = "markdown" -version = "3.3.7" +version = "3.4" description = "Python implementation of Markdown." -category = "dev" +category = "main" optional = false -python-versions = ">=3.6" +python-versions = ">=3.7" [package.dependencies] importlib-metadata = {version = ">=4.4", markers = "python_version < \"3.10\""} @@ -461,7 +496,7 @@ testing = ["coverage", "pytest", "pytest-cov", "pytest-regressions"] name = "markupsafe" version = "2.1.1" description = "Safely add untrusted strings to HTML/XML markup." -category = "dev" +category = "main" optional = false python-versions = ">=3.7" @@ -493,7 +528,7 @@ python-versions = ">=3.7" name = "mergedeep" version = "1.3.4" description = "A deep merge function for 🐍." -category = "dev" +category = "main" optional = false python-versions = ">=3.6" @@ -501,7 +536,7 @@ python-versions = ">=3.6" name = "mkdocs" version = "1.3.0" description = "Project documentation with Markdown." -category = "dev" +category = "main" optional = false python-versions = ">=3.6" @@ -522,9 +557,9 @@ i18n = ["babel (>=2.9.0)"] [[package]] name = "mkdocs-material" -version = "8.3.3" +version = "8.3.9" description = "Documentation that simply works" -category = "dev" +category = "main" optional = false python-versions = ">=3.7" @@ -540,10 +575,27 @@ pymdown-extensions = ">=9.4" name = "mkdocs-material-extensions" version = "1.0.3" description = "Extension pack for Python Markdown." -category = "dev" +category = "main" optional = false python-versions = ">=3.6" +[[package]] +name = "mkdocs-mermaid2-plugin" +version = "0.6.0" +description = "A MkDocs plugin for including mermaid graphs in markdown sources" +category = "main" +optional = false +python-versions = ">=3.5" + +[package.dependencies] +beautifulsoup4 = ">=4.6.3" +jsbeautifier = "*" +mkdocs = ">=1.0.4" +mkdocs-material = "*" +pymdown-extensions = ">=8.0" +pyyaml = "*" +requests = "*" + [[package]] name = "myst-parser" version = "0.18.0" @@ -582,7 +634,7 @@ et-xmlfile = "*" name = "packaging" version = "21.3" description = "Core utilities for Python packages" -category = "dev" +category = "main" optional = false python-versions = ">=3.6" @@ -607,18 +659,14 @@ python-versions = "*" [[package]] name = "prefixcommons" -version = "0.1.9" -description = "Library for working prefixcommons.org CURIEs" +version = "0.1.11" +description = "A python API for working with ID prefixes" category = "main" optional = false -python-versions = "*" +python-versions = ">=3.7,<4.0" [package.dependencies] -pyyaml = "*" -requests = "*" - -[package.extras] -test = ["pytest"] +requests = ">=2.28.1,<3.0.0" [[package]] name = "pydantic" @@ -639,7 +687,7 @@ email = ["email-validator (>=1.0.3)"] name = "pygments" version = "2.12.0" description = "Pygments is a syntax highlighting package written in Python." -category = "dev" +category = "main" optional = false python-versions = ">=3.6" @@ -659,7 +707,7 @@ jsonasobj = ">=1.2.1" name = "pymdown-extensions" version = "9.5" description = "Extension pack for Python Markdown." -category = "dev" +category = "main" optional = false python-versions = ">=3.7" @@ -724,7 +772,7 @@ shexjsg = ">=0.8.1" name = "python-dateutil" version = "2.8.2" description = "Extensions to the standard Python datetime module" -category = "dev" +category = "main" optional = false python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7" @@ -751,7 +799,7 @@ python-versions = ">=3.6" name = "pyyaml-env-tag" version = "0.1" description = "A custom YAML tag for referencing environment variables in YAML files. " -category = "dev" +category = "main" optional = false python-versions = ">=3.6" @@ -801,7 +849,7 @@ rdflib-jsonld = "0.6.1" [[package]] name = "requests" -version = "2.28.0" +version = "2.28.1" description = "Python HTTP for Humans." category = "main" optional = false @@ -809,13 +857,13 @@ python-versions = ">=3.7, <4" [package.dependencies] certifi = ">=2017.4.17" -charset-normalizer = ">=2.0.0,<2.1.0" +charset-normalizer = ">=2,<3" idna = ">=2.5,<4" urllib3 = ">=1.21.1,<1.27" [package.extras] socks = ["PySocks (>=1.5.6,!=1.5.7)"] -use_chardet_on_py3 = ["chardet (>=3.0.2,<5)"] +use_chardet_on_py3 = ["chardet (>=3.0.2,<6)"] [[package]] name = "ruamel.yaml" @@ -867,6 +915,14 @@ category = "dev" optional = false python-versions = "*" +[[package]] +name = "soupsieve" +version = "2.3.2.post1" +description = "A modern CSS selector implementation for Beautiful Soup." +category = "main" +optional = false +python-versions = ">=3.6" + [[package]] name = "sparqlslurper" version = "0.5.1" @@ -899,7 +955,7 @@ pandas = ["pandas (>=1.3.5)"] [[package]] name = "sphinx" -version = "5.0.1" +version = "5.0.2" description = "Python documentation generator" category = "dev" optional = false @@ -931,7 +987,7 @@ test = ["pytest (>=4.6)", "html5lib", "cython", "typed-ast"] [[package]] name = "sphinx-click" -version = "4.1.0" +version = "4.3.0" description = "Sphinx extension that automatically documents click applications" category = "dev" optional = false @@ -1015,7 +1071,7 @@ test = ["pytest"] [[package]] name = "sqlalchemy" -version = "1.4.37" +version = "1.4.39" description = "Database Abstraction Library" category = "dev" optional = false @@ -1048,7 +1104,7 @@ sqlcipher = ["sqlcipher3-binary"] [[package]] name = "typing-extensions" -version = "4.2.0" +version = "4.3.0" description = "Backported and Experimental Type Hints for Python 3.7+" category = "main" optional = false @@ -1056,11 +1112,11 @@ python-versions = ">=3.7" [[package]] name = "urllib3" -version = "1.26.9" +version = "1.26.10" description = "HTTP library with thread-safe connection pooling, file post, and more." category = "main" optional = false -python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, <4" +python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*, !=3.5.*, <4" [package.extras] brotli = ["brotlicffi (>=0.8.0)", "brotli (>=1.0.9)", "brotlipy (>=0.6.0)"] @@ -1069,9 +1125,9 @@ socks = ["PySocks (>=1.5.6,!=1.5.7,<2.0)"] [[package]] name = "watchdog" -version = "2.1.8" +version = "2.1.9" description = "Filesystem events monitoring" -category = "dev" +category = "main" optional = false python-versions = ">=3.6" @@ -1088,15 +1144,15 @@ python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,>=2.7" [[package]] name = "zipp" -version = "3.8.0" +version = "3.8.1" description = "Backport of pathlib-compatible object wrapper for zip files" category = "main" optional = false python-versions = ">=3.7" [package.extras] -docs = ["sphinx", "jaraco.packaging (>=9)", 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