diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..8e69e07 --- /dev/null +++ b/.gitignore @@ -0,0 +1,2 @@ +/.idea + diff --git a/README.md b/README.md index 6238865..b1fce74 100644 --- a/README.md +++ b/README.md @@ -1,39 +1,5 @@ -# BioPAX.org -(http://biopax.github.io) +# BioPAX GitHub organization website -Biological Pathways Exchange (BioPAX) is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. It is an open and collaborative effort by the community of researchers, software developers, and institutions. BioPAX is defined in [OWL DL](http://www.w3.org/TR/owl-features/) and is represented in the RDF/XML format. [BioPAX Paper](http://www.nature.com/nbt/journal/v28/n9/full/nbt.1666.html) was published in Nature Biotechnology in 2010. +See the result page at https://biopax.github.io but better go to www.biopax.org -## "Hello World" example: -``` - - - - - - - Hello World! - - -``` - -## Links: -* BioPAX ontology and documentation [releases](http://www.biopax.org/release/) -* BioPAX ontology [visualization](http://vowl.visualdataweb.org/webvowl/#iri=http://www.biopax.org/release/biopax-level3.owl) using WebVOWL (cool!) -* BioPAX secification [sub-project](https://github.com/BioPAX/specification) -* BioPAX model [examples](https://github.com/BioPAX/specification/blob/master/Level3/examples/) -* BioPAX [archive and downloads](http://www.biopax.org/downloads/biopax/) - -## PS: - -Official BioPAX web site www.biopax.org has been at CBIO MSKCC until 2013; -then it was moved to Sourceforge (Project-Web hosting, FRS, biopax.sf.net). -Now, we are migrating from Sourceforge. - - -Sincerely yours, - -BioPAX team. +The [BioPAX Paper](http://www.nature.com/nbt/journal/v28/n9/full/nbt.1666.html) diff --git a/_config.yml b/_config.yml index af6bf67..ad33326 100644 --- a/_config.yml +++ b/_config.yml @@ -1,3 +1,2 @@ -gems: - - jekyll-redirect-from - +#gems: +# - jekyll-redirect-from diff --git a/biopax-validator.md b/biopax-validator.md deleted file mode 100644 index cde7478..0000000 --- a/biopax-validator.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -redirect_from: - - "/biopax-validator" - - "/biopax-validator/" -redirect_to: - - http://biopax.baderlab.org/ ---- diff --git a/downloads.md b/downloads.md deleted file mode 100644 index 23d309f..0000000 --- a/downloads.md +++ /dev/null @@ -1,8 +0,0 @@ ---- -redirect_from: - - "/downloads" - - "/Downloads" - - "/download" - - "/Download" -redirect_to: http://sourceforge.net/projects/biopax/files/ ---- diff --git a/index.html b/index.html index cb92e5c..53b2e76 100644 --- a/index.html +++ b/index.html @@ -8,12 +8,7 @@ - - - - BioPAX (on Github) + BioPAX @@ -29,32 +24,32 @@

Biological Pathway Exchange

-

Biological Pathway Exchange (BioPAX) is a standard language that aims to enable integration, exchange, visualization and analysis - of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity - of interchange between data formats by providing an accepted standard format for pathway data. It is an open and collaborative effort - by the community of researchers, software developers, and institutions. BioPAX is defined in - OWL DL and is represented in the RDF/XML format. For more details, see - Demir E et al. 2010. The BioPAX community standard for pathway data sharing, Nature Biotechnology. 28(9). -

- +

Biological Pathway Exchange (BioPAX) is a standard language that aims to enable integration, exchange, visualization and analysis + of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity + of interchange between data formats by providing an accepted standard format for pathway data. It is an open and collaborative effort + by the community of researchers, software developers, and institutions. BioPAX is defined in + OWL DL and is represented in the RDF/XML format. For more details, see + Demir E et al. 2010. The BioPAX community standard for pathway data sharing, Nature Biotechnology. 28(9). +

+

Links:

@@ -63,37 +58,37 @@ 

<?xml version="1.0" encoding="UTF-8"?>
-          <rdf:RDF
-          xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
-          xmlns:owl="http://www.w3.org/2002/07/owl#"
-          xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
-          xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xml:base="">
-          <owl:Ontology rdf:about="">
-          <owl:imports rdf:resource="http://www.biopax.org/release/biopax-level3.owl#" />
-          </owl:Ontology>
-            <bp:Protein rdf:about="http://my.example.com/biopax#HelloWorld">
-              <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hello World!</bp:displayName>
-            </bp:Protein>
-          </rdf:RDF>
+<rdf:RDF
+xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
+xmlns:owl="http://www.w3.org/2002/07/owl#"
+xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
+xmlns:bp="http://www.biopax.org/release/biopax-level3.owl#" xml:base="">
+<owl:Ontology rdf:about="">
+<owl:imports rdf:resource="http://www.biopax.org/release/biopax-level3.owl#" />
+</owl:Ontology>
+  <bp:Protein rdf:about="http://my.example.com/biopax#HelloWorld">
+    <bp:displayName rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Hello World!</bp:displayName>
+  </bp:Protein>
+</rdf:RDF>

More examples examples

- +

Scientific Advisory Board

-

  • Gary Bader, University of Toronto
    • -
  • Peter D'Eustachio, New York University
    • -
  • Henning Hermjakob, European Bioinformatics Institute
    • -
  • Nicolas LeNovere, European Bioinformatics Institute
    • -
  • Peter Karp, SRI International
    • -
  • Chris Sander Harvard University
    • -

    +
  • Gary Bader, University of Toronto
    • +
  • Peter D'Eustachio, New York University
    • +
  • Henning Hermjakob, European Bioinformatics Institute
    • +
  • Nicolas LeNovere, European Bioinformatics Institute
    • +
  • Peter Karp, SRI International
    • +
  • Chris Sander Harvard University
    • +

    +
    - -
    @@ -104,7 +99,7 @@

    Scientific Advisory Board

    diff --git a/m2repo.md b/m2repo.md deleted file mode 100644 index ddbab5c..0000000 --- a/m2repo.md +++ /dev/null @@ -1,6 +0,0 @@ ---- -redirect_from: - - "/m2repo" - - "/m2repo/" -redirect_to: http://biopax.sourceforge.net/m2repo/ ---- diff --git a/params.json b/params.json deleted file mode 100644 index 84fb0ff..0000000 --- a/params.json +++ /dev/null @@ -1 +0,0 @@ -{"name":"BioPAX","tagline":"Biological Pathways Exchange language (RDF/XML)","body":"# BioPAX.org\r\n(biopax.github.io)\r\n\r\nBiological Pathways Exchange (BioPAX) is a standard language that aims to enable integration, exchange, visualization and analysis of biological pathway data. Specifically, BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. It is an open and collaborative effort by the community of researchers, software developers, and institutions. BioPAX is defined in [OWL DL](http://www.w3.org/TR/owl-features/) and is represented in the RDF/XML format. [BioPAX Paper](http://www.nature.com/nbt/journal/v28/n9/full/nbt.1666.html) was published in Nature Biotechnology in 2010.\r\n\r\n## \"Hello World\" example:\r\n```\r\n\r\n\r\n\r\n \r\n\r\n \r\n Hello World!\r\n \r\n\r\n```\r\n\r\n## Links:\r\n* BioPAX ontology and documentation [releases](http://www.biopax.org/release/)\r\n* BioPAX secification [sub-project](https://github.com/BioPAX/specification)\r\n* BioPAX model [examples](https://github.com/BioPAX/specification/blob/master/Level3/examples/)\r\n* BioPAX [archive and downloads](http://www.biopax.org/downloads/biopax/)\r\n \r\n## PS:\r\nOfficial BioPAX web site www.biopax.org has been at CBIO MSKCC until 2013; \r\nthen it moved to Sourceforge (Project-Web hosting, biopax.sf.net) and still resides there. \r\nSite configuration and some static content are stored in the Hg [repository](http://hg.code.sf.net/p/biopax/site).\r\nAnd we are thinking of a better design (not using .htaccess, MediaWiki and PHP) and migrating here.\r\n\r\n\r\nSincerely yours,\r\n\r\nBioPAX team.\r\n","google":"UA-43341809-1","note":"Don't delete this file! It's used internally to help with page regeneration."} \ No newline at end of file diff --git a/paxtools.md b/paxtools.md deleted file mode 100644 index 7962588..0000000 --- a/paxtools.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -redirect_from: - - "/paxtools" - - "/paxtools.php" - - "/Paxtools.php" -redirect_to: https://BioPAX.github.io/Paxtools/ ---- diff --git a/wiki.md b/wiki.md deleted file mode 100644 index 2dd938d..0000000 --- a/wiki.md +++ /dev/null @@ -1,7 +0,0 @@ ---- -redirect_from: - - "/mediawiki" - - "/wiki" - - "/biopaxwiki" -redirect_to: http://biopax.sourceforge.net/mediawiki/ ----