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2. PREFIX

The first part of most queries is the listing of one or more prefixes:

PREFIX mebase: <http://rdf.myexperiment.org/ontologies/base/>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>

SELECT ?a ?text
WHERE {
  ?a rdf:type mebase:Announcement .
  ?a mebase:text ?text
}
[Run]
[Hide Example Results]
atext
http://www.myexperiment.org/announcements/6

myExperiment is discussed by Jim Hendler in his article Reinventing Academic Publishing, Part 3 in IEEE Intelligent Systems January/February 2008, page 2-3.

http://www.myexperiment.org/announcements/29

A new project to link the myExperiment system with two existing electronic laboratory notebook (ELN) systems developed in Southampton, currently in use in several departments, has been announced today (June 11, 2009). By integrating these ELNs with myExperiment we will pave the way for longer term takeup in the experimental laboratory science communities, including Chemistry, Physics, Biology and Engineering.

The project will commence in July 2009 and will be led by Prof Jeremy Frey, who is based in the School of Chemistry at Southampton and is one of the partners in the myGrid Platform.

For more info please see http://wiki.myexperiment.org/index.php/MyExperimentalScience

-- Dave

http://www.myexperiment.org/announcements/14

We're pleased to announce that we've remodelled the myexperiment wiki to support the myExperiment developer community.

There is now a Developers' section where those of you developing over the API can share information about your projects.  It currently includes Google gadgets, the Taverna plugin, workflows for Facebook and the Java API.  This section also carries information about people running their own myExperiments, and myExperiment developer documentation.

The other information is now organised into Users, News and About. Previously you needed a wiki account to get at anything other than the main page, but now everything is publicly available, so you won't need to use your old accounts.

 

We’re really keen that everyone working over the API uses the wiki, if only to list who you are and what you’re doing – then all the developers will be able to help out as the community grows.

To get an account so that you can contribute content to the Developer pages please email Don Cruickshank on dgc@ecs.soton.ac.uk

http://www.myexperiment.org/announcement/3

In true 'perpetual beta' fashion, we continue our updates and additions to myExperiment:

  • In the user profile page, you can now see how many times a user has been credited for Workflows and Files in myExperiment. You can also see these credited items directly in the new "Creditations" tab, when viewing a user's profile.
  • Clearer statistics in the Workflow, File and User pages.
  • Improved layout for the Workflow and File pages.

Feedback always welcome!

http://www.myexperiment.org/announcement/25

Our paper "Software Design for Empowering Scientists", which discusses the design principles of Taverna and myExperiment, has appeared in the January/February 2009 issue of IEEE Software ("Developing Scientific Software, Part 2"). The article is available to subscribers on http://www2.computer.org/portal/web/csdl/doi/10.1109/MS.2009.22 and the preprint is available on http://eprints.ecs.soton.ac.uk/15032/  The full reference is

De Roure, D. and Goble, C. Software Design for Empowering Scientists, IEEE Software, Volume 26, Issue 1, Jan-Feb 2009, pages 88-95. Digital Object Identifier 10.1109/MS.2009.22

Also, myExperiment, along with OpenWetWare and nanoHub, feature in the article "Research intelligence - Log on to a global laboratory" in the January 1st issue of THE (Times Higher Education) , written by Sarah Collinson and Zoe Corbyn.  You can find the article on http://www.timeshighereducation.co.uk/story.asp?sectioncode=26&storycode=404834

...and Happy New Year to all our users!

-- Dave

Prefixes are not required within a query they just save rewriting the namespace each time you need to use it in a query and it makes the query easier to read. The previous query could be re-written as follows if you didn't want to use prefixes:

SELECT ?a ?text
WHERE {
  ?a <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> 
    <http://rdf.myexperiment.org/ontologies/base/Announcement> .
  ?a <http://rdf.myexperiment.org/ontologies/base/text> ?text
}

[Run]
[Hide Example Results]
atext
http://www.myexperiment.org/announcements/6

myExperiment is discussed by Jim Hendler in his article Reinventing Academic Publishing, Part 3 in IEEE Intelligent Systems January/February 2008, page 2-3.

http://www.myexperiment.org/announcements/29

A new project to link the myExperiment system with two existing electronic laboratory notebook (ELN) systems developed in Southampton, currently in use in several departments, has been announced today (June 11, 2009). By integrating these ELNs with myExperiment we will pave the way for longer term takeup in the experimental laboratory science communities, including Chemistry, Physics, Biology and Engineering.

The project will commence in July 2009 and will be led by Prof Jeremy Frey, who is based in the School of Chemistry at Southampton and is one of the partners in the myGrid Platform.

For more info please see http://wiki.myexperiment.org/index.php/MyExperimentalScience

-- Dave

http://www.myexperiment.org/announcements/14

We're pleased to announce that we've remodelled the myexperiment wiki to support the myExperiment developer community.

There is now a Developers' section where those of you developing over the API can share information about your projects.  It currently includes Google gadgets, the Taverna plugin, workflows for Facebook and the Java API.  This section also carries information about people running their own myExperiments, and myExperiment developer documentation.

The other information is now organised into Users, News and About. Previously you needed a wiki account to get at anything other than the main page, but now everything is publicly available, so you won't need to use your old accounts.

 

We’re really keen that everyone working over the API uses the wiki, if only to list who you are and what you’re doing – then all the developers will be able to help out as the community grows.

To get an account so that you can contribute content to the Developer pages please email Don Cruickshank on dgc@ecs.soton.ac.uk

http://www.myexperiment.org/announcement/3

In true 'perpetual beta' fashion, we continue our updates and additions to myExperiment:

  • In the user profile page, you can now see how many times a user has been credited for Workflows and Files in myExperiment. You can also see these credited items directly in the new "Creditations" tab, when viewing a user's profile.
  • Clearer statistics in the Workflow, File and User pages.
  • Improved layout for the Workflow and File pages.

Feedback always welcome!

http://www.myexperiment.org/announcement/25

Our paper "Software Design for Empowering Scientists", which discusses the design principles of Taverna and myExperiment, has appeared in the January/February 2009 issue of IEEE Software ("Developing Scientific Software, Part 2"). The article is available to subscribers on http://www2.computer.org/portal/web/csdl/doi/10.1109/MS.2009.22 and the preprint is available on http://eprints.ecs.soton.ac.uk/15032/  The full reference is

De Roure, D. and Goble, C. Software Design for Empowering Scientists, IEEE Software, Volume 26, Issue 1, Jan-Feb 2009, pages 88-95. Digital Object Identifier 10.1109/MS.2009.22

Also, myExperiment, along with OpenWetWare and nanoHub, feature in the article "Research intelligence - Log on to a global laboratory" in the January 1st issue of THE (Times Higher Education) , written by Sarah Collinson and Zoe Corbyn.  You can find the article on http://www.timeshighereducation.co.uk/story.asp?sectioncode=26&storycode=404834

...and Happy New Year to all our users!

-- Dave

2.1. BASE

The BASE clause is similar to the PREFIX clause but a name is not required, just the URI path needs be defined. If you wish to use the BASE clause it must proceed any PREFIX clauses. A common use of the BASE clause is to define the path for data that is being queried. E.g.

po
http://purl.org/dc/terms/modified2007-11-13T16:16:54Z
http://purl.org/dc/terms/hasFormathttp://www.myexperiment.org/workflow.xml?id=12
http://purl.org/dc/terms/hasFormathttp://www.myexperiment.org/workflows/12.rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#typehttp://rdf.myexperiment.org/ontologies/contributions/Workflow
http://purl.org/dc/terms/titleTranscribe a DNA sequence into an RNA sequence
http://xmlns.com/foaf/0.1/homepagehttp://www.myexperiment.org/workflows/12.html
http://purl.org/dc/terms/created2007-10-03T18:35:58Z
http://purl.org/dc/terms/descriptionThis workflow transcribes a DNA sequence into an RNA sequence
http://rdfs.org/sioc/ns#has_ownerhttp://www.myexperiment.org/users/43
http://rdf.myexperiment.org/ontologies/base/content-urlhttp://www.myexperiment.org/workflows/12/download/transcribe_a_dna_sequence_into_an_rna_sequence_27205.xml
http://rdf.myexperiment.org/ontologies/base/has-content-typehttp://www.myexperiment.org/content_types/1
http://rdf.myexperiment.org/ontologies/base/filenametranscribe_a_dna_sequence_into_an_rna_sequence_27205.xml
http://rdf.myexperiment.org/ontologies/base/has-policyhttp://www.myexperiment.org/workflows/12/policies/180
http://rdf.myexperiment.org/ontologies/base/has-licensehttp://www.myexperiment.org/licenses/1
http://rdf.myexperiment.org/ontologies/annotations/has-tagginghttp://www.myexperiment.org/tags/544/taggings/236
http://rdf.myexperiment.org/ontologies/annotations/has-tagginghttp://www.myexperiment.org/tags/547/taggings/300
http://rdf.myexperiment.org/ontologies/annotations/has-tagginghttp://www.myexperiment.org/tags/409/taggings/234
http://rdf.myexperiment.org/ontologies/annotations/has-tagginghttp://www.myexperiment.org/tags/214/taggings/299
http://rdf.myexperiment.org/ontologies/annotations/has-tagginghttp://www.myexperiment.org/tags/497/taggings/235
http://rdf.myexperiment.org/ontologies/annotations/has-tagginghttp://www.myexperiment.org/tags/119/taggings/301
http://rdf.myexperiment.org/ontologies/annotations/has-tagginghttp://www.myexperiment.org/tags/542/taggings/302
http://rdf.myexperiment.org/ontologies/viewings_downloads/downloaded630
http://rdf.myexperiment.org/ontologies/viewings_downloads/viewed887
http://www.openarchives.org/ore/terms/isDescribedByhttp://www.myexperiment.org/atom_entries/workflows/12
http://www.openarchives.org/ore/terms/isDescribedByhttp://www.myexperiment.org/resource_maps/workflows/12
http://rdf.myexperiment.org/ontologies/contributions/thumbnailhttp://www.myexperiment.org/workflow/image/12/thumb/transcribe_a_dna_sequence_into_an_rna_sequence_27205.png
http://rdf.myexperiment.org/ontologies/components/executes-dataflowhttp://www.myexperiment.org/workflows/12/versions/2/dataflow
http://rdf.myexperiment.org/ontologies/contributions/svghttp://www.myexperiment.org/workflow/svg/12/transcribe_a_dna_sequence_into_an_rna_sequence_27205.svg
http://rdf.myexperiment.org/ontologies/contributions/previewhttp://www.myexperiment.org/workflow/image/12/transcribe_a_dna_sequence_into_an_rna_sequence_27205.png
http://rdf.myexperiment.org/ontologies/base/has-current-versionhttp://www.myexperiment.org/workflows/12/versions/2
http://rdf.myexperiment.org/ontologies/base/last-edited-byhttp://www.myexperiment.org/users/43
http://rdf.myexperiment.org/ontologies/contributions/thumbnail-bighttp://www.myexperiment.org/workflow/image/12/medium/transcribe_a_dna_sequence_into_an_rna_sequence_27205.png
http://rdf.myexperiment.org/ontologies/base/has-versionhttp://www.myexperiment.org/workflows/12/versions/1
http://rdf.myexperiment.org/ontologies/annotations/has-commenthttp://www.myexperiment.org/users/9/favourites/5
http://rdf.myexperiment.org/ontologies/annotations/has-commenthttp://www.myexperiment.org/workflows/27/comments/92
http://rdf.myexperiment.org/ontologies/annotations/has-commenthttp://www.myexperiment.org/workflows/27/comments/275
http://rdf.myexperiment.org/ontologies/annotations/has-commenthttp://www.myexperiment.org/users/1634/favourites/47
http://rdf.myexperiment.org/ontologies/annotations/has-ratinghttp://www.myexperiment.org/workflows/27/ratings/59
http://rdf.myexperiment.org/ontologies/annotations/has-ratinghttp://www.myexperiment.org/workflows/27/ratings/15

Could be rewritten:

BASE <http://www.myexperiment.org/>
SELECT ?p ?o
WHERE{
  <workflows/12> ?p ?o
}
[Run]
[Hide Example Results]
po
http://purl.org/dc/terms/modified2007-11-13T16:16:54Z
http://purl.org/dc/terms/hasFormathttp://www.myexperiment.org/workflow.xml?id=12
http://purl.org/dc/terms/hasFormathttp://www.myexperiment.org/workflows/12.rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#typehttp://rdf.myexperiment.org/ontologies/contributions/Workflow
http://purl.org/dc/terms/titleTranscribe a DNA sequence into an RNA sequence
http://xmlns.com/foaf/0.1/homepagehttp://www.myexperiment.org/workflows/12.html
http://purl.org/dc/terms/created2007-10-03T18:35:58Z
http://purl.org/dc/terms/descriptionThis workflow transcribes a DNA sequence into an RNA sequence
http://rdfs.org/sioc/ns#has_ownerhttp://www.myexperiment.org/users/43
http://rdf.myexperiment.org/ontologies/base/content-urlhttp://www.myexperiment.org/workflows/12/download/transcribe_a_dna_sequence_into_an_rna_sequence_27205.xml
http://rdf.myexperiment.org/ontologies/base/has-content-typehttp://www.myexperiment.org/content_types/1
http://rdf.myexperiment.org/ontologies/base/filenametranscribe_a_dna_sequence_into_an_rna_sequence_27205.xml
http://rdf.myexperiment.org/ontologies/base/has-policyhttp://www.myexperiment.org/workflows/12/policies/180
http://rdf.myexperiment.org/ontologies/base/has-licensehttp://www.myexperiment.org/licenses/1
http://rdf.myexperiment.org/ontologies/annotations/has-tagginghttp://www.myexperiment.org/tags/544/taggings/236
http://rdf.myexperiment.org/ontologies/annotations/has-tagginghttp://www.myexperiment.org/tags/547/taggings/300
http://rdf.myexperiment.org/ontologies/annotations/has-tagginghttp://www.myexperiment.org/tags/409/taggings/234
http://rdf.myexperiment.org/ontologies/annotations/has-tagginghttp://www.myexperiment.org/tags/214/taggings/299
http://rdf.myexperiment.org/ontologies/annotations/has-tagginghttp://www.myexperiment.org/tags/497/taggings/235
http://rdf.myexperiment.org/ontologies/annotations/has-tagginghttp://www.myexperiment.org/tags/119/taggings/301
http://rdf.myexperiment.org/ontologies/annotations/has-tagginghttp://www.myexperiment.org/tags/542/taggings/302
http://rdf.myexperiment.org/ontologies/viewings_downloads/downloaded630
http://rdf.myexperiment.org/ontologies/viewings_downloads/viewed887
http://www.openarchives.org/ore/terms/isDescribedByhttp://www.myexperiment.org/atom_entries/workflows/12
http://www.openarchives.org/ore/terms/isDescribedByhttp://www.myexperiment.org/resource_maps/workflows/12
http://rdf.myexperiment.org/ontologies/contributions/thumbnailhttp://www.myexperiment.org/workflow/image/12/thumb/transcribe_a_dna_sequence_into_an_rna_sequence_27205.png
http://rdf.myexperiment.org/ontologies/components/executes-dataflowhttp://www.myexperiment.org/workflows/12/versions/2/dataflow
http://rdf.myexperiment.org/ontologies/contributions/svghttp://www.myexperiment.org/workflow/svg/12/transcribe_a_dna_sequence_into_an_rna_sequence_27205.svg
http://rdf.myexperiment.org/ontologies/contributions/previewhttp://www.myexperiment.org/workflow/image/12/transcribe_a_dna_sequence_into_an_rna_sequence_27205.png
http://rdf.myexperiment.org/ontologies/base/has-current-versionhttp://www.myexperiment.org/workflows/12/versions/2
http://rdf.myexperiment.org/ontologies/base/last-edited-byhttp://www.myexperiment.org/users/43
http://rdf.myexperiment.org/ontologies/contributions/thumbnail-bighttp://www.myexperiment.org/workflow/image/12/medium/transcribe_a_dna_sequence_into_an_rna_sequence_27205.png
http://rdf.myexperiment.org/ontologies/base/has-versionhttp://www.myexperiment.org/workflows/12/versions/1
http://rdf.myexperiment.org/ontologies/annotations/has-commenthttp://www.myexperiment.org/users/9/favourites/5
http://rdf.myexperiment.org/ontologies/annotations/has-commenthttp://www.myexperiment.org/workflows/27/comments/92
http://rdf.myexperiment.org/ontologies/annotations/has-commenthttp://www.myexperiment.org/workflows/27/comments/275
http://rdf.myexperiment.org/ontologies/annotations/has-commenthttp://www.myexperiment.org/users/1634/favourites/47
http://rdf.myexperiment.org/ontologies/annotations/has-ratinghttp://www.myexperiment.org/workflows/27/ratings/59
http://rdf.myexperiment.org/ontologies/annotations/has-ratinghttp://www.myexperiment.org/workflows/27/ratings/15
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