From 9474e2b4b3ff2f1d755002285b4db747df05e967 Mon Sep 17 00:00:00 2001 From: Charles Tapley Hoyt Date: Sun, 9 Oct 2022 17:39:24 +0200 Subject: [PATCH] Fall cleaning (#2122) * Begin fall cleaning * Add additional registry hints for products * Cleanup python validation * Consolidate logos folder into images folder * Clean up README text * More README cleanup * Move related projects * Delete remaining legacy * Delete browse.html * Update resources.md * Update validate-metadata.py * Simplify docs * Update how-do-i-edit-metadata.md * Update README.md Co-authored-by: Nico Matentzoglu * Update README-sitedev.md * Update README.md * Update resources.md Co-authored-by: Nico Matentzoglu --- README-sitedev.md | 46 +-- README.md | 132 +------ _layouts/browse_layout.html | 26 -- browse.html | 41 --- faq/how-do-i-edit-metadata.md | 30 +- {logos => images}/envo.png | Bin legacy/crit.html | 38 -- legacy/literature.html | 586 ------------------------------- legacy/participate.html | 57 --- legacy/publications.html | 94 ----- legacy/relatedprojects.html | 37 -- legacy/resources.html | 40 --- ontology/amphx.md | 2 +- ontology/envo.md | 2 +- sparql/ontology-contact.sparql | 11 - util/schema/registry_schema.json | 6 + util/validate-metadata.py | 16 +- 17 files changed, 58 insertions(+), 1106 deletions(-) delete mode 100644 _layouts/browse_layout.html delete mode 100644 browse.html rename {logos => images}/envo.png (100%) delete mode 100644 legacy/crit.html delete mode 100644 legacy/literature.html delete mode 100644 legacy/participate.html delete mode 100644 legacy/publications.html delete mode 100644 legacy/relatedprojects.html delete mode 100644 legacy/resources.html delete mode 100644 sparql/ontology-contact.sparql diff --git a/README-sitedev.md b/README-sitedev.md index 155142e8e..455a34c2b 100644 --- a/README-sitedev.md +++ b/README-sitedev.md @@ -1,41 +1,21 @@ -This documentation is for developers of this prototype OBO Foundry site. +# Site Development -Note this document is in markdown and is best viewed on GitHub. +This documentation is for developers of this prototype OBO Foundry site. ## Getting Started -You will first need jekyll, which can be installed by the ruby [gem](https://rubygems.org/): - - gem install jekyll - -After checking out the code from GitHub, you can start a local server: - - jekyll serve - -(this must always be done from the top level) - -Then view http://127.0.0.1:4000 - -You can make changes locally (you will need to start jekyll again - no -hot fixes). - -If you commit and push, your change will be visible within a few -minutes on: http://obofoundry.github.io - -If this site becomes official we may want to institute policies for -the site: e.g. major new changes happen on forks/branches, with a -voting policy for merging these in. - -### Serving with Docker - Because Jekyll can be difficult to install, Docker provides an -alternative for running the `serve` command: +alternative for running the `serve` command, then open http://localhost:4000: ```shell -$ export JEKYLL_VERSION=3.5 -$ docker run --rm --volume="$PWD:/srv/jekyll" -p 4000:4000 -it jekyll/jekyll:$JEKYLL_VERSION jekyll serve +$ docker run --rm --volume="$PWD:/srv/jekyll" -p 4000:4000 -it jekyll/jekyll:3.5 jekyll serve ``` +You can make changes locally and the Docker image will automatically update. +When you're ready, you can commit to a new branch and send a pull request. +After it's accepted, it will be automatically built and deployed to +http://obofoundry.github.io in a few minutes. + ## Details The setup is fairly standard for Jekyll. We use Jekyll bootstrap @@ -141,13 +121,9 @@ We could in theory easily manage our principles here. E.g. one .md file per principle. I personally think this much better than the current wiki, but other opinions welcome. -### Bootstrap Conventions - -We use bootstrap 3, so far no themes. - ### Code quality 1. Install the Node Package Manager (NPM) following [these instructions](https://docs.npmjs.com/downloading-and-installing-node-js-and-npm) 2. Install the [node package exector (`npx`)](https://www.npmjs.com/package/npx) with NPM using `npm install npx` -2. Install [`prettier`](https://prettier.io) with NPM using `npm install prettier` -3. Run `prettier` from the root of the repository with `npx prettier --write .` +3. Install [`prettier`](https://prettier.io) with NPM using `npm install prettier` +4. Run `prettier` from the root of the repository with `npx prettier --write .` diff --git a/README.md b/README.md index 6a979b833..1dd1537d3 100644 --- a/README.md +++ b/README.md @@ -1,34 +1,17 @@ -[![Build Status](https://travis-ci.org/OBOFoundry/OBOFoundry.github.io.svg?branch=master)](https://travis-ci.org/OBOFoundry/OBOFoundry.github.io) +# OBO Foundry Registry and Website -## OBO Foundry Registry and Website +This is the registry and website for the OBO Foundry. It is deployed with GitHub +Pages and Jekyll to https://obofoundry.github.io and is then mapped to +https://obofoundry.org. -### What is this? +For most questions, see the main site FAQ at https://obofoundry.org/faq/. +For details on site development, please see [README-sitedev.md](README-sitedev.md) -This is the registry and website for the OBO Foundry. - -It uses GitHub pages and can be visible here: http://obofoundry.github.io/ - -We map http://obofoundry.org to this address. - -### How does it work? - -The source can be found on https://github.com/OBOFoundry/OBOFoundry.github.io - -It uses GitHub Pages/[Jekyll](https://en.wikipedia.org/wiki/Jekyll_%28software%29), -a popular static site generator. - -GitHub pages [are integrated with -github](https://help.github.com/articles/using-jekyll-with-pages/) -which means that the entire site can be seen on -http://obofoundry.github.io (we don't run a dedicated webserver) - -For more details see: [README-sitedev.md](README-sitedev.md) +## Contributing ### I have some comments -You can use the [issue -tracker](https://github.com/OBOFoundry/OBOFoundry.github.io/issues) -but you may want to hold off til things are more stable +You can use the [issue tracker](https://github.com/OBOFoundry/OBOFoundry.github.io/issues) ### I want to contribute @@ -49,7 +32,6 @@ See [CONTRIBUTING.md](CONTRIBUTING.md) * [ontology/uberon.md](ontology/uberon.md) * ... * [Makefile](Makefile) `<-- For compiling derived artefacts and running tests` - * [.travis.yml](.travis.yml) `<-- continuous integration config` * [_posts/](_posts) `<-- Blog posts/news` * [_layouts/](_layouts) `<-- Jekyll layouts` * [_includes/](_includes) `<-- Jekyll includes` @@ -67,14 +49,14 @@ For example: * [ontology/uberon.md](ontology/uberon.md) * [ontology/bfo.md](ontology/bfo.md) -Each md file consists of +Each `*.md` file consists of * YAML metadata * Markdown text to be shown on the page for that ontology For example: -``` +```markdown --- layout: ontology_detail id: aeo @@ -95,46 +77,25 @@ AEO is an ontology of anatomical structures that expands CARO, the Common Anatom The [aeo page](http://obofoundry.github.io/ontology/aeo.html) shows the structured info on the right and the formatted text on the right. (THIS IS A BAD EXAMPLE IT HAS NO FORMATTING) The YAML data is strictly vetted by OBO team. The Makefile takes care -of syntactic validation (the travis job runs `make test`). The OBO +of syntactic validation (the GitHub Actions runs `make test`). The OBO team ensures the content is correct, up to date and accurate. You can put any HTML or Markdown in the lower section - customize each ontology page! Note that each md file is the primary source for the metadata for each ontology. It may seem odd to mix the markdown in with the yaml, but in -practice this works well and is easy to mainpulate using the python +practice this works well and is easy to manipulate using the python script in the util/ directory. The one piece of visual info in the md is the `layout` field, which is necessary for Jekyll. - -### Generation of downstream artefacts - -OBO admins should periodically - - git pull - make - jekyll server - ## open 127.0.0.1:4000 in a web browser and spot-check changes - git commit -m 'regenerated derived files' -a - git push origin master - -See the `Makefile` for details. This will have the effect of -regenerating the main ontologies yaml (used by external consumers such -as OLS, as well as the central OBO library build), as well as the -GitHub pages `_config.yml` file. This last step is necessary to update -the front page. - -_Note_: This process works using Ruby 2.6.6 and Jekyll 4.2.0. We tried using Ruby 3.0, but the setup failed for various reasons (missing libraries, obsolete/removed methods). If you are using Mac OS, we recommend using [rvm](https://rvm.io/rvm/install) to install the Ruby version. - - #### RDF The yaml is all "YAML-LD" and can compile down to RDF/OWL using a generic translator (eg JENA) plus our context file. ### Community Contributions -Note that general OBO users are free to edit via the github web +Note that general OBO users are free to edit via the GitHub web interface and make a pull request. They can update their own entries, but they are also welcome to suggest changes elsewhere. @@ -145,10 +106,10 @@ For example: * [view ontology/uberon.md](https://github.com/OBOFoundry/OBOFoundry.github.io/blob/master/ontology/uberon.md) * [edit ontology/uberon.md](https://github.com/OBOFoundry/OBOFoundry.github.io/edit/master/ontology/uberon.md) -Note that joe randoms cannot just come in and update things. Anyone with a github ID can make [pull request](https://help.github.com/articles/using-pull-requests/) +Note that joe randoms cannot just come in and update things. Anyone with a GitHub account can make [pull request](https://help.github.com/articles/using-pull-requests/) (aka PR). It is up to the OBO team whether the PR may be merged or rejected. -Note that if you make a syntax error whilst editing, then the travis +Note that if you make a syntax error whilst editing, then the GitHub Actions check will fail. Your PR will have a big red X next to it, in which case the OBO team will not merge your PR. Don't worry, all you have to do is make further edits to fix the syntax error. @@ -174,7 +135,7 @@ Depending on the build configuration, this may also make additional files. See f * http://berkeleybop.org/ontologies/uberon/ -A http://berkeleybop.org/ontologies/ URL should never be handed out directly. This service exists so that: +A http://berkeleybop.org/ontologies/ URL should never be handed out directly. This service exists so that: * Un PURL-registered ontologies will have a fall-through * Registered PURL ontologies that do not want to take charge of either OBO or OWL generation will have a place to 302-redirect to @@ -185,63 +146,6 @@ This job will fail if ontologies marked as `infallible` fail. To debug, the full (Look for the text "should not fail") -## Adding news - -Simply add a post to the [_posts/](_posts/) directory - copy an exiting one if you like - -Posts can also be edited via the GH web interface, all posts are here: - -https://github.com/OBOFoundry/OBOFoundry.github.io/tree/master/_posts - -## Instructions for WebSite developers - -Consult online Jekyll docs for details. Basically you just do - - gem install jekyll - -(I am currently using Jekyll 4.2.0 on Ruby 2.6.6; I tried using Ruby 3.0, but the setup failed for various reasons (missing libraries, obsolete/removed methods). If you are using Mac OS, I recommend using [rvm](https://rvm.io/rvm/install) to install the Ruby version.) - -You can run a local test install from the top level directory - - jekyll serve - -Then open http://127.0.0.1:4000 - -Every commit is visible within a few minutes on: http://obofoundry.github.io - -You may want to work on a branch to avoid disrupting the live -site. Exact procedures for accepting changes back into master have yet -to be determined. See [CONTRIBUTING.md](CONTRIBUTING.md) for a draft. - -The setup is fairly standard for Jekyll. We use Jekyll bootstrap -(bootstrap 3). We try and keep things minimal so that the site will -work on github. Even if you have no knowledge of Jekyll, it is fairly -easy to introspect what is going on if you have done much CMS work or -web development. - -Basics: - - * source can be markdown or html - * Different styles of pages go in _layouts - * ... - -## Site FAQ - -See also the main FAQ on the website: this FAQ is for OBO internal people - -### It's missing feature X from the old site - -File an issue! Or better yet, make a change on a fork and make a PR! - -### Shouldn't we pull project data from the ontologies themselves? - -We should definitely have some mechanism for syncing these or allowing -this option. However, for the majority of ontologies for which I (cjm) -are de-facto administrating, the expertise and time to do this in OWL -is not there, and many groups prefer to have this centralized. - - - - - +## Instructions for Website Development +See [README-sitedev.md](README-sitedev.md) diff --git a/_layouts/browse_layout.html b/_layouts/browse_layout.html deleted file mode 100644 index fc199ada2..000000000 --- a/_layouts/browse_layout.html +++ /dev/null @@ -1,26 +0,0 @@ - - - - - - {{ page.title }} - - - - - - - - {% include navbar.html %} - -
-
-
-
{{ content }}
-
-
-
- - {% include footer.html %} - - diff --git a/browse.html b/browse.html deleted file mode 100644 index dea517c9a..000000000 --- a/browse.html +++ /dev/null @@ -1,41 +0,0 @@ ---- -layout: default -title: Browse ---- - -
- -
diff --git a/faq/how-do-i-edit-metadata.md b/faq/how-do-i-edit-metadata.md index 9819faa3f..fa1e61737 100644 --- a/faq/how-do-i-edit-metadata.md +++ b/faq/how-do-i-edit-metadata.md @@ -64,32 +64,24 @@ A few key properties to be aware of: ### Freeform Markdown -The section after the second `---` controls what goes in the main panel on your ontology page. You should include at least a one paragarph description here. You are free to put more detail, and you can use a mixture of HTML and Markdown formatting. You can even put images in here. +The section after the second `---` controls what goes in the main panel on your ontology page. You should include at least a one paragraph description here. You are free to put more detail, and you can use a mixture of HTML and Markdown formatting. You can even put images in here. You should not put citations, funding statements, or other information that is possible to include in the structured data. -For example, here is the ENVO freeform markdown section +For example, here is the AMPHX freeform markdown section -``` -EnvO is a community ontology for the concise, controlled description of environments. - - - -Envo can be cited as: - -Buttigieg, P. L., Morrison, N., Smith, B., Mungall, C. J., & Lewis, S. E. (2013). The environment ontology: contextualising biological and biomedical entities. Journal of Biomedical Semantics, 4(1), 43. doi:10.1186/2041-1480-4-43 +```markdown +The Amphioxus Development and Anatomy Ontology (AMPHX) is to describe the anatomy and development of Amphioxus, also known as lancelet, member of the invertebrate subphylum Cephalochordata and the phylum Chordata. This ontology is intended to be used for description of gene expression in amphioxus (e.g. Insitus, RNA-seq). The ontology was created in the context of the European project [CORBEL](https://www.corbel-project.eu/home.html), and used in the database [MARIMBA](http://marimba.obs-vlfr.fr/home). ``` ### Pull Request Pipeline -Any user can make propsed changes to any md file. These remain on -their fork until approved by OBO admins. - -The workflow is: +Any user can make proposed changes to any `*.md` file. These remain on +their fork until approved by OBO admins. The workflow is: -1. An automated Travis job will run to validate your changes -2. An OBO administrator will evaluate your PR. If it failed the travis check, it will not be accepted -3. If the the OBO admin rejects it they will provide feedback in the comment form which you can use to make further edits -4. More likely, the change will be accepted by the OBO admin. They will click "merge" and the changes will be visible in a few seconds. -5. The OBO admin will also need to run a Make script to regenerate the main metadata file, so your changes may not be visible on the front table straight away +1. An automated GitHub Actions job will run to validate your changes +2. An OBO administrator will evaluate your PR. If it failed the checks, it will not be accepted +3. If the the OBO admin rejects it they will provide feedback in the comment form which you can use to make further edits +4. More likely, the change will be accepted by the OBO admin. They will click "squash and merge". +5. An automated GitHub Actions workflow will update the build artifacts and issue a new PR. An OBO admin can review and accept. ## Pull Request Tutorial diff --git a/logos/envo.png b/images/envo.png similarity index 100% rename from logos/envo.png rename to images/envo.png diff --git a/legacy/crit.html b/legacy/crit.html deleted file mode 100644 index f5402fc78..000000000 --- a/legacy/crit.html +++ /dev/null @@ -1,38 +0,0 @@ -

- OBO is an open community and, by joining the initiative, the - authors of an ontology commit to its maintenance in light of - scientific advance and to working with other members to - ensure the improvement of these principles over time. The - OBO Foundry is an attempt to apply the scientific method to - the task of ontology development, and the scientific method - rests on constant criticism and on the assumption that no - resource will ever exist in a form in which it cannot be - further improved. -

-

Current Version

-

- The current list of OBO Foundry Principles are listed on - the OBO Foundry - Wiki: -

-

Current List of OBO Foundry Principles

-

- Note that as of July 2011, every principle has its own unique identifier. The principles are divided into two categories: -

-

-

- To comment on, or ask questions about, any of these - principles please send e-mail to - the - - OBO discussion list. - . -

-

Previous Versions

- - diff --git a/legacy/literature.html b/legacy/literature.html deleted file mode 100644 index e18a58b6d..000000000 --- a/legacy/literature.html +++ /dev/null @@ -1,586 +0,0 @@ ---- -layout: default -title: Literature ---- - -
- - Papers that cite the OBO Foundry -
- -

- Antezana E, Tsiporkova E, Mironov V, et al. 2006 "A - cell-cycle knowledge integration framework", Lecture Notes - in Computer Science 4075: 19-34. - - http://www.psb.ugent.be/cbd/cco/cellcycleframework.pdf - -

- -

- Aranguren ME, Bechoffer S, Lord P, Sattler U, Stevens R 2007 - "Understanding and using the meaning of statements in a - bio-ontology: recasting the Gene Ontology in OWL", BMC - Bioinformatics, 8: 57. - - http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1819394&blobtype=pdf - - -

- -

- Arnaiz O, Cain S, Cohen J, Sperling L 2006 "ParameciumDB: a - community resource that integrates the Paramecium - tetraurelia genome sequence with genetic data", Nucleic - Acids Res Dec 7. - - http://nar.oxfordjournals.org/cgi/screenpdf/35/suppl_1/D439 - -

- -

- Baker CJO, Shaban-Nejad A, Su X, Haarslev V, Butler G 2006 - "Semantic Web infrastructure for fungal enzyme - biotechnologists", J Web Semantics 4 (3). - - - http://users.encs.concordia.ca/~haarslev/publications/JWS-2006.pdf - -

- -

- Bard JBL 2005 "Anatomics: the intersection of anatomy and - bioinformatics", Journal of Anatomy 206 (1): 1-16 Jan. - - http://www.blackwell-synergy.com/doi/pdf/10.1111/j.0021-8782.2005.00376.x?cookieSet=1 - -

- -

- Bittner T, Goldberg LJ 2006 "The Qualitative and - Time-Dependent Character of Spatial Relations in Biomedical - Ontologies", O. Bodenreider, ed., Proceedings of KR-MED, - 47-55. - - http://www.acsu.buffalo.edu/~bittner3/BittnerGoldbergKRMed.pdf - -

- -

- Blake JA, Bult CJ 2006 "Beyond the data deluge: Data - integration and bio-ontologies", Journal of Biomedical - Informatics 39 (3): 314-320. - - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16564748 - - -

- -

- Bodenreider O. 2006 "Lexical, terminological and ontological - resources for biological text mining", in Ananiadou S, - McNaught J, (eds.) Text mining for biology and biomedicine, - Artech House, 43-66. - - http://lhncbc.nlm.nih.gov/lhc/docs/published/2006/pub2006007.pdf - -

- -

- Bontas EP, Schlangen D, Schrader T 2005 "Creating ontologies - for content representation - The OntoSeed suite", Lecture - Notes in Computer Science 3761: 1296-1313. - - - http://userpage.fu-berlin.de/~paslaru/papers/jods2006.pdf - -

- -

- Burek P, Hoehndorf R, Loebe F, Visagie J, Herre H Kelso - J. 2006 "A top-level ontology of functions and its - application in the Open Biomedical Ontologies", - Bioinformatics, Vol. 22 no. 14: e66-e73. - - http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/14/e66 - -

- -

- Castro AG, Rocca-Serra P, Stevens R, Taylor C, Nashar K, - Ragan MA, Sansone SA 2006 "The use of concept maps during - knowledge elicitation in ontology development processes--the - nutrigenomics use case", BMC Bioinformatics 25 (7): 267. - - http://www.biomedcentral.com/1471-2105/7/267/abstract - -

- -

- Ceusters W 2006 "Towards a Realism-Based Metric for Quality - Assurance in Ontology Matching", Formal Ontology in - Information Systems - Proceedings of the Fourth - International Conference (FOIS 2006), Edited by Brandon - Bennett, Christiane Fellbaum, New York: IOS Press, 321-332. - - http://ontology.buffalo.edu/bfo/Ontology_Matching.pdf - - -

- -

- Ceusters W, Smith B 2006 "A Realism-Based Approach to the - Evolution of Biomedical Ontologies", Proceedings of the - Annual AMIA Symposium, Washington DC, 121-125. - - http://ontology.buffalo.edu/bfo/Versioning.pdf - -

- -

- Dameron O, Roques E, Rubin DL, Marquet G, and Burgun A 2006 - "Grading lung tumors using OWL-DL based reasoning", In 9th - International Protégé Conference. - - http://www.med.univ-rennes1.fr/~dameron/publis/2006protege-dameron.pdf - -

- -

- Dolbey A, Ellsworth M, Scheffczyk J 2006 "BioFrameNet: A - Domain-Specific FrameNet Extension with Links to Biomedical - Ontologies", O. Bodenreider, ed., Proceedings of KR-MED, - 87-94. - - http://ftp.informatik.rwth-aachen.de/Publications/CEUR-WS/Vol-222/krmed2006-p10.pdf - -

- -

- Donnelly M, Bittner T, Rosse C 2006 "A formal theory for - spatial representation and reasoning in biomedical - ontologies", Artificial Intelligence in Medicine 36 (1): - 1-27. - - http://www.acsu.buffalo.edu/~md63/DonnellyAIMed05.pdf - -

- -

- Friedberg I 2006 "Automated protein function prediction - - the genomic challenge", Briefings in Bioinformatics 7 (3): - 225-242. - - https://academic.oup.com/bib/article/7/3/225/326173 - - -

- -

- Friedman C, Borlawsky T, Shagina L, et al. 2006 - "Bio-Ontology and text: bridging the modeling gap", - Bioinformatics 22 (19): 2421-2429. - - http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/19/2421 - -

- -

- Fung KW, et al. 2005 "Integrating SNOMED CT into the UMLS: An Exploration of Different Views of Synonymy and Quality of Editing", Am Med Inform Assoc. - - - http://www.jamia.org/cgi/reprint/12/4/486.pdf - - -

-

- Gardner SP 2005 "Ontologies and semantic data integration", Drug Discovery Today, 10 (14): 1001-1007. - - http://64.233.179.104/scholar?hl=en&lr=&safe=off&q=cache:RXb5cPWct5IJ:www.biowisdom.co.uk/docs/DDT_Ontologies_and_Semantic_Integ\ - ration.pdf+ - - -

- -

- Gkoutos, GV 2006 "Towards a phenotypic semantic web", - Current Bioinformatics, 1 (2): 235-246. - - - http://www.ingentaconnect.com/content/ben/cbio/2006/00000001/00000002/art00010 - -

- -

- Haendel, MA, Neuhaus, F, Osumi-Sutherland, DS, Mabee, PM, - Mejino JLV, Mungall, CJ, and Smith, B - 2007 "The Common Anatomy Reference - Ontology", in: A Burger, et al. (eds.), Anatomy Ontologies - for Bioinformatics: Principles and Practice, New York, - Springer. - - http://www.acsu.buffalo.edu/~fneuhaus/caropreprint.pdf -

- -

- Hahn U, Schulz S, 2007 "Ontological Foundations for Biomedical Sciences", in - Artificial Intelligence in Medicine, 39 (3): 179-82. - - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Abstract&list_uids=17321117 - - -

- -

- Harris MA, Clark JI, Ireland A, et al./Gene Ontology Consortium. 2006 "The Gene Ontology (GO) project in 2006", Nucleic Acids Research 34: D322-D326 Sp. Iss. SI Jan1. - - http://nar.oxfordjournals.org/cgi/screenpdf/34/suppl_1/D322.pdf - -

-

- Henrich T, Ramialison M, Wittbrodt B, Assouline B, Bourrat F, Berger - A, Himmelbauer H, Sasaki T, Shimizu N, Westerfield M, Kondoh H, and - Wittbrodt J 2005 "MEPD: a resource for medaka gene expression patterns", - Bioinformatics 2005 21(14):3195-3197; doi:10.1093/bioinformatics/bti478 . - - http://bioinformatics.oxfordjournals.org/cgi/content/abstract/21/14/3195 - -

- -

- Hsing, M., Cherkasov, A. 2006 "Integration of Biological - Data with Semantic Networks", Current Bioinformatics, 1 (3): - 273-290. - - - http://colab.cim3.net/file/work/SICoP/2006-10-10/Hsing_CBIO.pdf - -

- -

- Ingenerf J., Linder R. 2006 "Ontological Principles Applied - to Biomedical Vocabularies". - - http://www.imbi.uni-freiburg.de/medinf/fctc-2006/docs/in_final.pdf - -

- -

- Johansson I. 2006 "Bioinformatics and biological reality", - Journal of Biomedical Informatics 39 (3): 274-287. - - http://hem.passagen.se/ijohansson/information4.PDF - -

- -

- Kosseim L, Reda Siblini, Christopher J.O. Baker and Sabine - Bergler 2006 "Using Selectional Restrictions to Query an OWL - Ontology", Formal Ontology in Information Systems - - Proceedings of the Fourth International Conference (FOIS - 2006), Edited by Brandon Bennett, Christiane Fellbaum, New - York: IOS Press, 360-371. - - http://users.encs.concordia.ca/~kosseim/Publications/fois2006.pdf - - -

- -

- Louie B, Mork P, Martin-Sanchez F, et al. 2007 "Data integration and genomic medicine", Journal of Biomedical Informatics, 40 (1): 5-16. - - - http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6WHD-4JF8G2S-1&_user=681891&_coverDate=02%2F28%2F2007&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000037419&_version=1&_urlVersion=0&_userid=681891&md5=79d8eb7d16f9905770ba994d169d1e8d - -

-

- Mabee PM, Arratia G, Coburn M, Haendel M, Hilton EJ, Lundberg JG, Mayden RL, Rios N, and Westerfield M 2007 "Connecting evolutionary morphology to genomics using ontologies: A case study from Cypriniformes including zebrafish", J Exp Zoolog B Mol Dev Evol. 2007 Sep 15;308(5):655-6. - -

-

- Maglia AM, et al. 2007 "An anatomical ontology for amphibians", Pacific Symposium on Biocomputing, 12: 367-378. - - - http://psb.stanford.edu/psb-online/proceedings/psb07/maglia.pdf - - -

-

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- - Myhre S, Tveit H, Mollestad T, et al. 2006 "Additional Gene Ontology structure for improved biological reasoning", Bioinformatics 22 (16): 2020-2027. - - - http://bioinformatics.oxfordjournals.org/cgi/reprint/22/16/2020 - - -

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- DA Natale, CN Arighi, W Barker, J Blake, TC Chang, Z Hu, H Liu, B Smith, and CH Wu 2006 - "Framework for a Protein Ontology", - Proceedings of the 1st international workshop on Text mining in bioinformatics, Arlington, Virginia, 29-36. - - - http://pir.georgetown.edu/pirwww/about/doc/tmbio19-natale.pdf - - -

-

- Neuhaus F, et al. - "Modelling Principles and Methodologies: Relations in Anatomical Ontologies", in: A Burger et al. (eds.), Anatomy Ontologies for Bioinformatics: Principles and Practice, New York: Springer, in press. -

-

- - Okada M, Sugimoto Y, Yoshikawa S, et al. 2006 "Drug Interaction Ontology (DIO) and the resource-sensitive logical inferences", Lecture Notes in Computer Science; 4060: 616-642. -

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- Paul S, et al. 2006 "A semantically enabled formalism for the knowledge management of Parkinson's disease". Medical Informatics and the Internet in Medicine. - - - http://www.informaworld.com/smpp/content?content=10.1080/14639230500299220 - - -

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- Philippi S, Kohler J 2006 "Addressing the problems with life-science databases for traditional uses and systems biology", Nature Reviews Genetics 7 (6): 482-488. - - - http://www.nature.com/nrg/journal/v7/n6/abs/nrg1872.html - - -

-

- - Rogers JE 2006 "Quality assurance of medical ontologies", Methods of Information in Medicine 45 (3): 267-274. - - - http://www.schattauer.de/index.php?id=1268&pii=me06030267&no_cache=1 - - -

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- Rosenbloom ST, Miller RA, Johnson KB, et al. 2006 "Interface terminologies: Facilitating direct entry of clinical data into electronic health record systems", Journal of the American Medical Informatics Association 13 (3): 277-288. - - - http://www.jamia.org/cgi/reprint/13/3/277 - - -

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- Ruttenberg A, Clark T, et al. 2007 "Advancing translational research with the Semantic Web", BMC Bioinformatics, 8(Suppl 3):S2. - - - - http://www.biomedcentral.com/1471-2105/8/S3/S2 - - -

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- Ruttenberg A, Rees J, Zucker J. 2007 "What BioPAX communicates and how to extend OWL to help it", OWLED. - - - - http://www.webont.org/owled/2006/acceptedLong/submission_26.pdf - - -

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- Schulz S, Elena Beisswanger, Udo Hahn, Joachim Wermter, Anand Kumar and Holger Stenzhorn 2006 "From GENIA to BIOTOP: Towards a Top-Level Ontology for Biology", Formal Ontology in Information Systems - Proceedings of the Fourth International Conference (FOIS 2006), Ed. by B. Bennett, C. Fellbaum, New York: IOS Press, 103-114. - - - http://www.ifomis.uni-saarland.de/people/holger/publications/fois06.pdf - - -

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- -

- Zhou L, Tao Y, Cimino JJ, et al. 2006 "Terminology model - discovery using natural language processing and - visualization techniques", Journal of Biomedical Informatics - 39 (6): 626-636. - - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=16360342 - -

- diff --git a/legacy/participate.html b/legacy/participate.html deleted file mode 100644 index 4f0b24751..000000000 --- a/legacy/participate.html +++ /dev/null @@ -1,57 +0,0 @@ ---- -layout: default -title: Participate ---- - -
- Participation in the OBO Foundry -
- -

Join

-

- How any group that is in the process of developing an - ontology and who would like to join the foundry can do this. -

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- - OBO Wiki - -

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- Not much here yet, but contributions are welcome. If you - would like an account on the wiki, please contact the - . -

- -

- - Discussion - -

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- A list of all of the OBO Foundry discussion lists, archives, - and how to subscribe. -

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- Click here to subscribe (or unsubscribe) to the primary OBO - discussion list. -

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diff --git a/legacy/publications.html b/legacy/publications.html deleted file mode 100644 index f372588f8..000000000 --- a/legacy/publications.html +++ /dev/null @@ -1,94 +0,0 @@ ---- -layout: default -title: Publications ---- - -

Citing OBO

- -

- OBO, an integrative multi-species anatomy - ontology Mungall, C. J., Torniai, C., Gkoutos, G. V., Lewis, S. E., and - Haendel, M. A. (2012) Genome Biology 13, R5. PMID:22293552 -

-

- -Unification of multi-species vertebrate anatomy ontologies for comparative biology in OBO -Haendel, Melissa A; -Balhoff, James P; -Bastian, Frederic B; -Blackburn, David C; -Blake, Judith A; -Bradford, Yvonne; -Comte, Aurelie; -Dahdul, Wasila M; -Dececchi, Thomas A; -Druzinsky, Robert E; -Hayamizu, Terry F; -Ibrahim, Nizar; -Lewis, Suzanna E; -Mabee, Paula M; -Niknejad, Anne; -Robinson-Rechavi, Marc; -Sereno, Paul C; -Mungall, Christopher J -(2014) -Journal of Biomedical Semantics, 5(1), 21. doi:10.1186/2041-1480-5-21 -

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- All papers referencing OBO -
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Mendeley Group

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Posters and Presentatations

- - diff --git a/legacy/relatedprojects.html b/legacy/relatedprojects.html deleted file mode 100644 index 1c23b874f..000000000 --- a/legacy/relatedprojects.html +++ /dev/null @@ -1,37 +0,0 @@ -

Generic Model Organism Databases

-

- The Generic Model Organism Project (GMOD) is a joint effort by the model organism system databases WormBase, FlyBase, MGI, SGD, Gramene, Rat Genome Database, EcoCyc, and TAIR to develop reusable components suitable for creating new community databases of biology. -

-

Ontologies for Biomedical Investigations

-

- The Ontology for Biomedical Investigations (OBI) project is developing an integrated ontology for the description of biological and medical experiments and investigations. This ontology will support the consistent annotation of biomedical investigations, regardless of the particular field of study. -

-

Institute for Formal Ontology and Medical Information Science - (IFOMIS)

-

- The Institute for Formal Ontology and Medical Information Science - (IFOMIS) comprehends an interdisciplinary research group with members - from Philosophy, Computer and Information Science, Logic, Medicine, - and Medical Informatics, focusing on theoretically grounded research - in both formal and applied ontology. -

-

MGED

-

- The Microarray Gene Expression Data (MGED) Society is an international organisation of biologists, computer scientists, and data analysts that aims to facilitate the sharing of microarray data generated by functional genomics and proteomics experiments. -

-

Ontology Lookup Service

-

- The Ontology Lookup Service is a spin-off of the PRIDE project, which required a centralized query interface for ontology and controlled vocabulary lookup. While many of the ontologies queriable by the OLS are available online, each has its own query interface and output format. The OLS provides a web service interface to query multiple ontologies from a single location with a unified output format. -

-

Plant Ontology Consortium

-

- The Plant Ontology Consortium (POC) aims to develop, curate and share structured controlled vocabularies (ontologies) that describe plant structures and growth/developmental stages. Through this effort, the project aims to facilitate cross database querying by fostering consistent use of these vocabularies in the annotation of tissue and/or growth stage specific expression of genes, proteins and phenotypes. -

-

Proteomics Standards Initiative

-

- Is also interested in guidelines for the development of Controlled Vocabularies. -

-

Standards and Ontologies for Functional Genomics

-

- SOFG is both a meeting and a website; it aims to bring together biologists, bioinformaticians, and computer scientists who are developing and using standards and ontologies with an emphasis on describing high-throughput functional genomics experiments. -

diff --git a/legacy/resources.html b/legacy/resources.html deleted file mode 100644 index b2f009afc..000000000 --- a/legacy/resources.html +++ /dev/null @@ -1,40 +0,0 @@ -

- - Mappings - -

-

- On this page you can find bi-directional mappings between - OBO ontologies and from OBO ontologies to other - ontologies (or controlled vocabularies) that are critical to - the biomedical research community. Useful for the - integration of data. -

- -

- Tools - -

-

- Just one tool listed here now--OBO-Edit, a graphical tool for - creating and updating ontologies. More tools are coming soon. -

- -

- - Literature - -

-

- A compendium of relevant publications that mention the OBO Foundry. -

- -

- - Project - -

-

- The OBO Foundry uses SourceForge to manage this - project. This is a link to the SourceForge project page for OBO. -

diff --git a/ontology/amphx.md b/ontology/amphx.md index be2ff2bce..ecd61c5a1 100644 --- a/ontology/amphx.md +++ b/ontology/amphx.md @@ -28,4 +28,4 @@ tracker: https://github.com/EBISPOT/amphx_ontology/issues activity_status: active --- -The Amphioxus Development and Anatomy Ontology (AMPHX) is to describe the anatomy and development of Amphioxus, also known as lancelet, member of the invertebrate subphylum Cephalochordata and the phylum Chordata. This ontology is intended to be used for description of gene expression in amphioxus (e.g. Insitus, RNA-seq). The ontology was created in the context of the European project CORBEL (https://www.corbel-project.eu/home.html), and used in the database MARIMBA (http://marimba.obs-vlfr.fr/home). +The Amphioxus Development and Anatomy Ontology (AMPHX) is to describe the anatomy and development of Amphioxus, also known as lancelet, member of the invertebrate subphylum Cephalochordata and the phylum Chordata. This ontology is intended to be used for description of gene expression in amphioxus (e.g. Insitus, RNA-seq). The ontology was created in the context of the European project [CORBEL](https://www.corbel-project.eu/home.html), and used in the database [MARIMBA](http://marimba.obs-vlfr.fr/home). diff --git a/ontology/envo.md b/ontology/envo.md index c24b3070a..99cacc2fe 100644 --- a/ontology/envo.md +++ b/ontology/envo.md @@ -23,7 +23,7 @@ dependencies: - id: po - id: ro - id: uberon -depicted_by: /logos/envo.png +depicted_by: /images/envo.png description: An ontology of environmental systems, components, and processes. domain: environment homepage: http://environmentontology.org/ diff --git a/sparql/ontology-contact.sparql b/sparql/ontology-contact.sparql deleted file mode 100644 index f3e2425a3..000000000 --- a/sparql/ontology-contact.sparql +++ /dev/null @@ -1,11 +0,0 @@ -prefix owl: -prefix rdfs: -prefix dce: -prefix dcat: - -SELECT ?ont ?name WHERE -{ - ?ont dcat:contactPoint ?person . - ?person rdfs:label ?name - -} diff --git a/util/schema/registry_schema.json b/util/schema/registry_schema.json index 734126734..f1ac259a1 100644 --- a/util/schema/registry_schema.json +++ b/util/schema/registry_schema.json @@ -339,6 +339,12 @@ "id": { "type": "string", "pattern": "^[0-9A-Za-z-_\\/]+\\.(owl|obo|json|omn|ofn|owx|ttl|owl\\.gz)$" + }, + "title": { + "type": "string" + }, + "description": { + "type": "string" } }, "required": [ diff --git a/util/validate-metadata.py b/util/validate-metadata.py index 63920cc4b..2d55cf249 100755 --- a/util/validate-metadata.py +++ b/util/validate-metadata.py @@ -1,7 +1,6 @@ #!/usr/bin/env python3 import json -import os import re import sys from argparse import ArgumentParser @@ -28,7 +27,7 @@ } -def main(args): +def main(): global metadata_grid parser = ArgumentParser( description=""" @@ -97,8 +96,8 @@ def load_data(yaml_infile): def get_schema(): """Return a schema from the master schema directory.""" schema = None + file = SCHEMA_FILE try: - file = SCHEMA_FILE with open(file, "r") as s: schema = json.load(s) except Exception as e: @@ -151,11 +150,16 @@ def validate_metadata(item, schema): else: path = ["properties", title] abs_schema = schema + level = None for schema_item in path: if schema_item in abs_schema: if "level" in abs_schema[schema_item]: level = abs_schema[schema_item]["level"] abs_schema = abs_schema[schema_item] + if level is None: + raise ValueError + else: + raise ValueError # add to the results map results[title] = level @@ -179,7 +183,7 @@ def validate_metadata(item, schema): if not ( ( item.get("activity_status") == "orphaned" - and title in ["contact", "license", "license-lite"] + and title in ["contact", "license"] ) or ( item.get("is_obsolete") is True @@ -190,7 +194,7 @@ def validate_metadata(item, schema): ): # get a message for displaying on terminal msg = ve.message - if title in ["license", "license-lite"]: + if title in ["license"]: # license error message can show up in a few different ways search = re.search("'(.+?)' is not one of", msg) if search: @@ -383,4 +387,4 @@ def save_results(results, violations_outfile): if __name__ == "__main__": - main(sys.argv) + main()