MyExperiment
{{Use dmy dates|date=April 2022}}
{{lowercase title|myExperiment}}
{{infobox biodatabase
|title = myExperiment
|logo =300px
|description = myExperiment
|scope =
|organism =
|center =Department of Computer Science, University of Manchester
|laboratory =
|author =
|citation = Goble & al. (2010){{Cite journal
| last1 = Goble | first1 = C. A.
| author-link1 = Carole Goble
| last2 = Bhagat | first2 = J.
| last3 = Aleksejevs | first3 = S.
| last4 = Cruickshank | first4 = D.
| last5 = Michaelides | first5 = D.
| last6 = Newman | first6 = D.
| last7 = Borkum | first7 = M.
| last8 = Bechhofer | first8 = S.
| last9 = Roos | first9 = M.
| last10 = Li
| doi = 10.1093/nar/gkq429 | first10 = P.
| last11 = De Roure | first11 = D.
| title = MyExperiment: A repository and social network for the sharing of bioinformatics workflows
| journal = Nucleic Acids Research
| volume = 38
| issue = Web Server issue
| pages = W677–W682
| year = 2010
| pmid = 20501605
| pmc =2896080
}}
|released =
|standard =
|format =
|url = http://www.myexperiment.org
|download =
|webservice =
|sql =
|sparql =
|webapp =
|standalone =
|license =
|versioning =
|frequency =
|curation =
|bookmark =
|version=
}}myExperiment is a social web site for researchers sharing research objects such as scientific workflows.{{Cite journal | last1 = Bechhofer | first1 = S. | last2 = Buchan | first2 = I. | last3 = De Roure | first3 = D. | author-link3 = David De Roure| last4 = Missier | first4 = P. | last5 = Ainsworth | first5 = J. | last6 = Bhagat | first6 = J. | last7 = Couch | first7 = P. | last8 = Cruickshank | first8 = D. | last9 = Delderfield | first9 = M. | last10 = Dunlop | first10 = I. | last11 = Gamble | first11 = M. | last12 = Michaelides | first12 = D. | last13 = Owen | first13 = S. | last14 = Newman | first14 = D. | last15 = Sufi | first15 = S. | last16 = Goble | first16 = C. | title = Why linked data is not enough for scientists | doi = 10.1016/j.future.2011.08.004 | journal = Future Generation Computer Systems | volume = 29 | issue = 2 | pages = 599 | year = 2011 | s2cid = 16783450 | url = https://eprints.soton.ac.uk/271587/1/research-objects-final.pdf }}{{Cite journal | last1 = De Roure | first1 = D. | author-link1 = David De Roure| last2 = Goble | first2 = C. | author-link2 = Carole Goble| last3 = Stevens | first3 = R.| author-link3 = Robert David Stevens | doi = 10.1016/j.future.2008.06.010 | title = The design and realisation of the myExperiment Virtual Research Environment for social sharing of workflows | journal = Future Generation Computer Systems | volume = 25 | issue = 5 | pages = 561–567 | year = 2009 | url = https://eprints.soton.ac.uk/265709/1/fgcs.pdf }}{{Cite book | last1 = Roure | first1 = D. D. | title = 2008 IEEE Fourth International Conference on e Science | author-link1 = David De Roure| last2 = Goble | first2 = C. | author-link2 = Carole Goble| last3 = Bhagat | first3 = J. | last4 = Cruickshank | first4 = D. | last5 = Goderis | first5 = A. | last6 = Michaelides | first6 = D. | last7 = Newman | first7 = D. | doi = 10.1109/eScience.2008.86 | chapter = MyExperiment: Defining the Social Virtual Research Environment | pages = 182–189 | year = 2008 | isbn = 978-1-4244-3380-3 | s2cid = 11104419 | url = https://eprints.soton.ac.uk/266560/1/escimyexpv6.pdf }}{{Cite journal | last1 = De Roure | first1 = D. | author-link1 = David De Roure| last2 = Goble | first2 = C. | author-link2 = Carole Goble| doi = 10.1109/MS.2009.22 | title = Software Design for Empowering Scientists | journal = IEEE Software | volume = 26 | pages = 88–95 | year = 2009 | s2cid = 33191938 | url = https://eprints.soton.ac.uk/265032/1/myExpSoftwareFinal.pdf }}
The myExperiment website was launched in November 2007 and contains a significant collection of scientific workflows for a variety of workflow systems, most notably Taverna, but also other tools such as Bioclipse. myExperiment has a REST API and is based on an open source Ruby on Rails codebase. It supports Linked data and had a SPARQL Endpoint, with an interactive tutorial.{{cite web |title=How To SPARQL |url=http://rdf.myexperiment.org/howtosparql |website=myExperiment RDF |archive-url=https://web.archive.org/web/20190326134611/http://rdf.myexperiment.org/howtosparql |archive-date=2019-03-26}}{{Cite journal | last1 = Gewin | first1 = Virginia| title = The new networking nexus: A crop of websites is making networking among scientists easier than ever | doi = 10.1038/nj7181-1024a | journal = Nature | volume = 451 | issue = 7181 | pages = 1024–1025 | year = 2008 | pmid = 18363200}}{{Cite journal | last1 = Hendler | first1 = J. | author-link = James Hendler| doi = 10.1109/MIS.2008.12 | title = Reinventing Academic Publishing, Part 3 | journal = IEEE Intelligent Systems | volume = 23 | pages = 2–3 | year = 2008 | url = https://zenodo.org/record/895390 }}{{Cite journal | last1 = Stein | first1 = L. D. | author-link = Lincoln Stein| title = Towards a cyberinfrastructure for the biological sciences: Progress, visions and challenges | doi = 10.1038/nrg2414 | journal = Nature Reviews Genetics | volume = 9 | issue = 9 | pages = 678–688 | year = 2008 | pmid = 18714290| s2cid = 339653 }}
Origin
The myExperiment project was initially directed by David De Roure at University of Southampton (later University of Oxford) and was one of the activities of the myGrid consortium led by Carole Goble of The University of Manchester, UK and of the [https://archive.today/20121223184948/http://www.eresearchsouth.ac.uk/ e-Research South] UK regional consortium led by the [http://www.oerc.ox.ac.uk/ Oxford e-Research Centre]. It was originally funded by Jisc under the Virtual Research Environment programme and by the Microsoft [http://www.microsoft.com/mscorp/tc/ Technical Computing Initiative].
Capturing digital experiments
While the initial idea of myExperiment may have been to capture computational experiments as executions of registered workflows (submitted to a configured workflow runner API), in reality most users of myExperiment shared only workflow definitions, possibly with example files.
Influence on Research Objects development
The myExperiment Ontology {{cite web |title=myExperiment Ontology |url=http://rdf.myexperiment.org/ontologies/ |archive-url=https://web.archive.org/web/20190712173758/http://rdf.myexperiment.org/ontologies/ |archive-date=2019-07-12}} included details of social networking, attributions, experiments and workflow structures. This work was instrumental in forming the idea of Research Objects,{{Cite journal | last1 = Bechhofer | first1 = S. | last2 = Buchan | first2 = I. | last3 = De Roure | first3 = D. | author-link3 = David De Roure| last4 = Missier | first4 = P. | last5 = Ainsworth | first5 = J. | last6 = Bhagat | first6 = J. | last7 = Couch | first7 = P. | last8 = Cruickshank | first8 = D. | last9 = Delderfield | first9 = M. | last10 = Dunlop | first10 = I. | last11 = Gamble | first11 = M. | last12 = Michaelides | first12 = D. | last13 = Owen | first13 = S. | last14 = Newman | first14 = D. | last15 = Sufi | first15 = S. | last16 = Goble | first16 = C. | title = Why linked data is not enough for scientists | doi = 10.1016/j.future.2011.08.004 | journal = Future Generation Computer Systems | volume = 29 | issue = 2 | pages = 599 | year = 2011 | s2cid = 16783450 | url = https://eprints.soton.ac.uk/271587/1/research-objects-final.pdf }} a Linked Data method for identification, aggregation and exchange of scholarly information. In the myExperiment Ontology, the Research Object was loosely represented as a "Pack" of typed related resources, including workflows.
myExperiment was since enhanced by the Workflows Forever project (Wf4Ever){{cite web |url=http://www.wf4ever-project.org/ |archive-url=https://web.archive.org/web/20121107105528/http://www.wf4ever-project.org/ |archive-date=2012-11-07 |title=Home - wf4ever |access-date=2012-06-19}} which in 2011 aimed to provide new features to support the preservation of Research Objects in conjunction with the [https://dingo.psnc.pl/dlibra/ dLibra] digital library framework.https://www.newscientist.com/article/mg19225745.500-myspace-for-the-dudes-in-lab-coats.html MySpace for the dudes in lab coats in New Scientist magazine, issue 2574, page 29. 21 October 2006.http://www.timeshighereducation.co.uk/story.asp?storycode=404834 Times Higher Education article "Log on to a global laboratory: web 2.0 tools allow researchers to share ideas, data and results" by Sarah Collinson and Zoe Corbyn in the "Research intelligence" section, page 22 (1 January 2009).
The Wf4Ever co-development with the workflow system Taverna (at the time maintained by myGrid), led to the creation of the Research Object Model ontologies.{{cite journal |doi=10.1016/j.websem.2015.01.003|hdl=1887/78857|hdl-access=free}} RO Model uses many of the conceptual ideas of the myExperiment Ontology, but with a basis of an OAI-ORE aggregation as the central digital object, and with a primary goal of reproducibility and integration with the W3C provenance model PROV, the replacing RO Model was independent of the social network at a workflow registry.
In 2019, subsequent development of Research Object Crate (RO-Crate) replaced the RO Model with a profile of schema.org serialised in JSON-LD, this was general purpose for scholarly outputs. This ontology-less approach was better suitable for packaging in a ZIP archive and aimed to be more approachable for developers without Linked Data experience.{{cite journal |doi=10.3233/DS-210053|arxiv=2108.06503}}
Current status
The [https://www.myexperiment.org/ myexperiment.org] is as of 2024 hosted by University of Manchester, at professor Carole Goble's eScience Lab as a legacy service.{{cite web |title=myExperiment |url=https://esciencelab.org.uk/products/myexperiment/ |website=eScience Lab |access-date=2024-06-15}}
The research group has since launched{{cite web |url=https://esciencelab.org.uk/products/workflowhub/ |website=eScience Lab |title=WorkflowHub |access-date=2024-06-15}}{{cite web |title=WorkflowHub |url=https://www.openresearch.manchester.ac.uk/resources/case-studies/workflowhub/ |website=Office of Open Research |publisher=The University of Manchester |access-date=2024-06-15}} myExperiment's replacement, the workflow registry [https://workflowhub.eu/ workflowhub.eu],{{cite report |title=Implementing FAIR Digital Objects in the EOSC-Life Workflow Collaboratory |date=2021-03-21 |doi=10.5281/zenodo.4605654 |publisher=Zenodo}} which uses a profile of RO-Crate for publishing workflows together with their context and dependencies. In contrast with myExperiment, the WorkflowHub however do not focus on the social network aspects (beyond institutional/project organisation of entries), and do not attempt to capture any experiments.