From 78ff5faa41e2158f64cb00f45bcb81289f14b415 Mon Sep 17 00:00:00 2001 From: James Stevenson Date: Tue, 30 Jul 2024 15:59:58 -0400 Subject: [PATCH] additional work --- _includes/citation_toc.md | 11 +++++++ _includes/header.html | 7 ++--- _layouts/citation.html | 52 +++++++++++++++++++++++++++++++++ _layouts/ontology_detail.html | 2 +- assets/css/style.css | 9 ++++++ {docs => citation}/Citation.md | 33 ++++++++++++++------- citation/KnownPublications.md | 18 ++++++++++++ citation/RelatedPublications.md | 15 ++++++++++ registry/publications.md | 34 --------------------- 9 files changed, 132 insertions(+), 49 deletions(-) create mode 100644 _includes/citation_toc.md create mode 100644 _layouts/citation.html rename {docs => citation}/Citation.md (67%) create mode 100644 citation/KnownPublications.md create mode 100644 citation/RelatedPublications.md delete mode 100644 registry/publications.md diff --git a/_includes/citation_toc.md b/_includes/citation_toc.md new file mode 100644 index 000000000..9a977537c --- /dev/null +++ b/_includes/citation_toc.md @@ -0,0 +1,11 @@ +[OBO Citation and Attribution Policy](/citation/Citation.html) + +- [Referring to a single term](/citation/Citation.html#single-term) +- [Referring to an ontology](/citation/Citation.html#refer-ontology) +- [Citing an ontology](/citation/Citation.html#cite-ontology) + +[OBO Foundry Publications](/citation/RelatedPublications.html) +- [Citing the OBO Foundry](/citation/RelatedPublications.html#citing) +- [Other OBO Foundry Publications](/citation/RelatedPublications.html#other) + +[OBO Foundry Ontology Publications](/citation/KnownPublications.html) diff --git a/_includes/header.html b/_includes/header.html index 20d62b6df..36550c72d 100644 --- a/_includes/header.html +++ b/_includes/header.html @@ -113,10 +113,9 @@ Citation diff --git a/_layouts/citation.html b/_layouts/citation.html new file mode 100644 index 000000000..034f90170 --- /dev/null +++ b/_layouts/citation.html @@ -0,0 +1,52 @@ +--- +layout: default +--- +
+
+
+

{{ page.title }}

+
+
+ +
+
+
+ {% capture my_include %}{% include citation_toc.md %}{% endcapture %} {{ + my_include | markdownify }} {% if page.id %} +
+ + + + + + + +
+ {% endif %} +
+ +
{{ content }}
+
+
+
+ diff --git a/_layouts/ontology_detail.html b/_layouts/ontology_detail.html index ae0acadd4..ce3ce1289 100644 --- a/_layouts/ontology_detail.html +++ b/_layouts/ontology_detail.html @@ -84,7 +84,7 @@

- {% if page.publications %} + {% if page.publications and page.publications.size > 0 %}
Publications diff --git a/assets/css/style.css b/assets/css/style.css index a230117dc..f1b1484a1 100644 --- a/assets/css/style.css +++ b/assets/css/style.css @@ -34,3 +34,12 @@ Slightly darken failing ontologies .dash-status { margin-bottom: 3px; } + +/* +Custom blockquote formatting +*/ +.citation-blockquote { + padding: 5px; + margin-left: 20px; + margin-bottom: 16px; +} diff --git a/docs/Citation.md b/citation/Citation.md similarity index 67% rename from docs/Citation.md rename to citation/Citation.md index e15b6f7c4..104471012 100644 --- a/docs/Citation.md +++ b/citation/Citation.md @@ -1,46 +1,59 @@ --- -layout: doc +layout: citation title: OBO Citation and Attribution Policy --- Open Biological and Biomedical Ontologies are used in a diversity of ways. The following guidelines are intended to promote proper attribution of the ontology creators and contributors, and to promote reproducibility in informatics applications. -## Referring to a single term +

Referring to a single term

When referring to a single ontology term, use the full [Internationalized Resource Identifier (IRI)](http://tools.ietf.org/html/rfc3987), for example: -> http://purl.obolibrary.org/obo/UBERON_0000948 +
+http://purl.obolibrary.org/obo/UBERON_0000948 +
You can use a shorter [Compact URI (CURIE)](https://www.w3.org/TR/curie/) by defining a prefix that abbreviates the first part of the IRI. For example, the prefix "UBERON" can abbreviate "http://purl.obolibrary.org/obo/UBERON_", then "http://purl.obolibrary.org/obo/UBERON_0000948" can be shortened to "[UBERON:0000948](http://purl.obolibrary.org/obo/UBERON_0000948)". A footnote like this one should be included with the first use of the prefix: -> [UBERON:0000948](http://purl.obolibrary.org/obo/UBERON_0000948) is a Compact URI (CURIE). Here and subsequently the prefix "UBERON" expands to "http://purl.obolibrary.org/obo/UBERON_". The full identifier for the term is then . Browsing to this address gives further information about the term. +
+UBERON:0000948 is a Compact URI (CURIE). Here and subsequently the prefix "UBERON" expands to "http://purl.obolibrary.org/obo/UBERON_". The full identifier for the term is then http://purl.obolibrary.org/obo/UBERON_0000948. Browsing to this address gives further information about the term. +
In situations that allow the use of hyperlinks, every CURIE should be a hyperlink with its full IRI as its target, as in these examples. We also recommend including the primary label of the term in quotation marks before the IRI or CURIE: -> 'heart' ([UBERON:0000948](http://purl.obolibrary.org/obo/UBERON_0000948)) +
+'heart' (UBERON:0000948) +
-## Referring to an ontology +

Referring to an ontology

To facilitate reproducibility, be specific about the version of the ontology that you are referring to by using an ontology version IRI that contains the release date: -> http://purl.obolibrary.org/obo/uberon/releases/2016-01-26/uberon.owl +
+http://purl.obolibrary.org/obo/uberon/releases/2016-01-26/uberon.owl +
The ontology version IRI is indicated by the [owl:versionIRI](https://www.w3.org/2002/07/owl#versionIRI) property. When referring to an ontology in general (not a specific version) you can use its ontology IRI: -> http://purl.obolibrary.org/obo/uberon.owl +
+http://purl.obolibrary.org/obo/uberon.owl +
The ontology IRI or ontology version IRI should be accompanied by a citation of the ontology, in any context where citations are appropriate. -## Citing an ontology +

Citing an ontology

Some ontologies recommend citation of specific publications. Please see their respective homepages for this information. For example, [Uberon]({{ "ontology/uberon.html#publications" | prepend: site.baseurl }}) lists two publications under "Publications." In addition to the recommended publication, you should also cite the ontology using its IRI and the [new data citation extension to JATS](https://peerj.com/articles/cs-1/). When no specific publication is recommended, you must cite the ontology by its IRI. Here is an example citation: -> Mungall, C., Haendel, M., Dahdul, W., Ibrahim, N., Segerdell, E., Blackburn, D., Comte, A., Niknejad, A., and Decechi, A. (2016), Uberon Ontology, http://purl.obolibrary.org/obo/uberon/releases/2016-01-26/uberon.owl +
+Mungall, C., Haendel, M., Dahdul, W., Ibrahim, N., Segerdell, E., Blackburn, D., Comte, A., Niknejad, A., and Decechi, A. (2016), Uberon Ontology, http://purl.obolibrary.org/obo/uberon/releases/2016-01-26/uberon.owl +
Our ontology files list authors using the [dc:creator](http://purl.org/dc/elements/1.1/creator) property. The order of authors is not important, but you can use the primary contact for the ontology listed on the [OBO site](http://obofoundry.org) as the first author. Note that this does not necessarily include all those who have contributed directly to the ontology, via its issue tracker or on its mailing lists, for example. However, these can be readily retrieved if the proper IRI is referenced in the citation. + diff --git a/citation/KnownPublications.md b/citation/KnownPublications.md new file mode 100644 index 000000000..5032e8f75 --- /dev/null +++ b/citation/KnownPublications.md @@ -0,0 +1,18 @@ +--- +layout: citation +title: Known Ontology Project Publications +--- + +This list is generated automatically from OBO Foundry ontology metadata. It is not intended to be authoritative or exhaustive. +
+ {% for ontology in site.ontologies %} + {% if ontology.publications and ontology.publications.size > 0 %} +
{{ ontology.title }} ({{ ontology.id }})
+ + {% endif %} + {% endfor %} +
diff --git a/citation/RelatedPublications.md b/citation/RelatedPublications.md new file mode 100644 index 000000000..50f879cea --- /dev/null +++ b/citation/RelatedPublications.md @@ -0,0 +1,15 @@ +--- +layout: citation +title: Publications Related to the OBO Foundry +--- +

Citing the OBO Foundry

+ +To reference the OBO Foundry generally, please cite: + +Rebecca Jackson, Nicolas Matentzoglu, James A Overton, Randi Vita, James P Balhoff, Pier Luigi Buttigieg, Seth Carbon, Melanie Courtot, Alexander D Diehl, Damion M Dooley, William D Duncan, Nomi L Harris, Melissa A Haendel, Suzanna E Lewis, Darren A Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M Schriml, Barry Smith, Christian J Stoeckert Jr., Nicole A Vasilevsky, Ramona L Walls, Jie Zheng, Christopher J Mungall, Bjoern Peters, **[OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies](https://academic.oup.com/database/article/doi/10.1093/database/baab069/6410158)**, Database, Volume 2021, 2021, baab069, https://doi.org/10.1093/database/baab069 + +

Other papers about the OBO Foundry

+ +Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J Mungall, The OBI Consortium, Neocles Leontis, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H Scheuermann, Nigam Shah, Patricia L Whetzel, and Suzanna Lewis, **[The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration](http://www.nature.com/nbt/journal/v25/n11/abs/nbt1346.html)**, Nature Biotechnology, Volume 25, 2007, https://doi.org/10.1038/nbt1346 + +[Google Scholar list of papers citing The OBO Foundry](https://scholar.google.ca/scholar?cites=13806088078865650870&as_sdt=2005&sciodt=0,5&hl=en) diff --git a/registry/publications.md b/registry/publications.md deleted file mode 100644 index ec995ca2d..000000000 --- a/registry/publications.md +++ /dev/null @@ -1,34 +0,0 @@ ---- -layout: doc -title: Publications Related to the OBO Foundry ---- -## Citing the OBO Foundry - -[**OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies**](https://academic.oup.com/database/article/doi/10.1093/database/baab069/6410158) **(2021)**. - -Rebecca Jackson, Nicolas Matentzoglu, James A Overton, Randi Vita, James P Balhoff, Pier Luigi Buttigieg, Seth Carbon, Melanie Courtot, Alexander D Diehl, Damion M Dooley, William D Duncan, Nomi L Harris, Melissa A Haendel, Suzanna E Lewis, Darren A Natale, David Osumi-Sutherland, Alan Ruttenberg, Lynn M Schriml, Barry Smith, Christian J Stoeckert Jr., Nicole A Vasilevsky, Ramona L Walls, Jie Zheng, Christopher J Mungall, Bjoern Peters. *Database*, Volume 2021, baab069, https://doi.org/10.1093/database/baab069 - -## Other papers about the OBO Foundry - -[The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration](http://www.nature.com/nbt/journal/v25/n11/abs/nbt1346.html) - -Barry Smith, Michael Ashburner, Cornelius Rosse, Jonathan Bard, William Bug, Werner Ceusters, Louis J Goldberg, Karen Eilbeck, Amelia Ireland, Christopher J Mungall, The OBI Consortium, Neocles Leontis, Philippe Rocca-Serra, Alan Ruttenberg, Susanna-Assunta Sansone, Richard H Scheuermann, Nigam Shah, Patricia L Whetzel, and Suzanna Lewis - -*Nature Biotechnology* **25**, 1251 - 1255 (2007) - -[Google Scholar list of papers citing The OBO Foundry](https://scholar.google.ca/scholar?cites=13806088078865650870&as_sdt=2005&sciodt=0,5&hl=en) - -### Known Ontology Project Publications - -This list is generated automatically from OBO Foundry ontology metadata. It is not intended to be authoritative or exhaustive. - -
    -{% for ontology in site.ontologies %} -{% for publication in ontology.publications %} -
  • - {{ ontology.title }} ({{ ontology.id }}): - {{ publication.title }} -
    • -{% endfor %} -{% endfor %} -