Profile

Cover photo
Allyson Lister
Works at University of Oxford
Attended Newcastle University
7,881 followers|186,651 views
AboutPosts

Stream

Allyson Lister

Shared publicly  - 
 
Question for the ontologists out there! I've been trying to determine if two ontologies, originally developed by Thorsten Heinrich at EMBL Heidelberg, are still active? They were both developed by the 4DXpress group (http://4dx.embl.de/4DXpress/welcome.do), but emails to Thorsten Heinrich, Yannick Haudry, and indeed to info@emble.de result in either undeliverable mail or (in the case of info@embl.de) no reply.

Our entries for the two records which the 4DX group is associated with can be found here:

http://biosharing.org/bsg-000006 (BILA - Bilateria anatomy)
http://biosharing.org/bsg-000013 (PD_ST - Platynereis Developmental STage)

The BILA ontology is currently listed as inactive on its OBO Foundry page at http://obofoundry.org/cgi-bin/detail.cgi?id=bilateria_mrca, and the Platynereis is listed as under discussion (http://www.obofoundry.org/cgi-bin/detail.cgi?id=platynereis_stage_ontology). Neither are listed at all under BioPortal (http://bioportal.bioontology.org/).

Can anyone confirm with me if this ontology is no longer currently in development and you believe deprecation of this record within BioSharing would be appropriate? Is anyone using these ontologies? +Trish Whetzel please share with anyone you might think knows something about this :)

We do enjoy keeping our records up to date, and any help with this matter would be most appreciated. Thanks!
Search our 585 Standards, 664 Databases, 21 Policies, and 3 Views · View the content summary. A web-based, curated and searchable portal ensuring that standards, databases and policies in the life sciences are registered, informative and discoverable. Click to read more about BioSharing.
1
Add a comment...

Allyson Lister

Shared publicly  - 
 
Just started working with +Susanna-Assunta Sansone and her group on http://www.biosharing.org. As always, happy to chat about biological data standards - and now I'm back working in them too! https://themindwobbles.wordpress.com/2015/02/03/back-into-data-standards-with-biosharing/
7
Susanna-Assunta Sansone's profile photo
 
Welcome Allyson!
Add a comment...
 
Good morning all! I've been taking a look at ImpactStory (http://impactstory.org) and wondering if it's worth paying for. What do I get there that I don't get currently through 1) google scholar, 2) (the slightly odd) microsoft academic search, 3) linked in 4) research gate etc., all of which I get for free and to which I am already subscribed.

This of course leads to the bigger question of how many places do we need to maintain our research identity? Via my work persona, I do like to be available to other researchers interested in the same area of work, and therefore I am willing to maintain a number of social media outlets such as those above. However, where do we stop signing up for such things, and how do we know what's working best for us with respect to reaching out to the community of like-minded researchers?

Your thoughts would be most appreciated - thanks!

1. http://scholar.google.co.uk/citations?user=3gIIMLsAAAAJ&hl=en
2. http://academic.research.microsoft.com/Author/3762141
3. http://www.linkedin.com/profile/view?id=3123595
4. https://www.researchgate.net/profile/Allyson_Lister
3
Allyson Lister's profile photoJan Moren's profile photoAlejandra Gonzalez-Beltran's profile photo
 
 
We're organizing a biological data visualization course in November 2015. So please spread the word, and register for updates at http://bit.ly/datavizcourseleuven
View original post
1
1
David Nickerson's profile photo
Add a comment...

Allyson Lister

Shared publicly  - 
 
Segway's entry into SWO - +Michael Hoffman , please let me know if you wish a more precise assertion for any of the axioms present below...
1
Michael Hoffman's profile photoAllyson Lister's profile photo
4 comments
 
Updated all except output files - will post a new pic once I've included those tomorrow-ish. All in SVN though if you were interested ;) https://sourceforge.net/p/theswo/code/HEAD/tree/trunk/dev/ontologydev/
Add a comment...
 
What bioinformatics software would you consider a "must have" for a software ontology? Tell me and if it's not already in, I'll add it this week! :) http://softwareontology.wordpress.com/
1
Michael Hoffman's profile photoAllyson Lister's profile photo
2 comments
 
It's added in the latest development version, without a reference to the owning organization, as I wasn't sure what you wanted that to be? The Hoffman lab? A particular organization or group? To look at your software in OWL, you need to download *.owl from https://sourceforge.net/p/theswo/code/HEAD/tree/trunk/dev/ontologydev/ (It'll be in a nicer format with the next point release in the next week or two.
Add a comment...

Allyson Lister

Shared publicly  - 
 
Paper submission for the 10th Annual International Symposium on Integrative Bioinformatics has been extended until 3rd March 2014.

Please note that full papers will appear in a special edition of the Journal of Integrative Bioinformatics: http://journal.imbio.de/.
1
1
Randy Culp's profile photo
Add a comment...
Have her in circles
7,881 people
Donald Tassie's profile photo
Bill Meade's profile photo
Brett Szmajda's profile photo
Justin Lundsteen's profile photo
Jari Sundell's profile photo
Rizal Rashid's profile photo
Alec Brownstein's profile photo
Dennis Humble's profile photo
David Mikulin's profile photo
 

Very interesting user experience when trying to browse a few entries from the NAR database issue. As I've just started at BioSharing.org, it makes me think - just what would you all want in a standards and database registry? What would make you give full points to any particular entry? Yes, working URLs are a big thing, but what would the killer feature be for you? Examples, high numbers of cross references, contact points for owners of the entries? Please let me know! HT +Alejandra Gonzalez-Beltran 
Something interesting happened in 2014. The total number of databases that Nucleic Acids Research (NAR) tracks dropped by three databases! What happened?  Did people quit making databases?  No.  This year, the “dead” databases (links no longer valid) outnumber the new ones. To celebrate Digital World Biology’s release of Molecule World I’ll discuss some of the new structure databases…
1
Add a comment...

Allyson Lister

Shared publicly  - 
 
University of Oxford Job Opportunity: Research Software Engineer - Java, Python, Web-app, Database, Semantic-web

In this varied, interesting and challenging role the successful candidate will provide technical knowledge, software engineering and leadership ability for (i) a growing portfolio of data and knowledge management projects - including the ISA software suite (http://isacommons.org), the BioSharing registry (http://biosharing.org) - funded by UK, EU and NIH Big Data to Knowledge Initiative, and (i) activities for the ELIXIR UK node (http://elixir-uk.org) of the ELIXIR programme.

Job title: Research Software Engineer
Location: University of Oxford, Oxford e-Research Centre, 7 Keble Road, Oxford, OX1 3QG, UK
Contract type: 3 years fixed term, in the first instance (salary range £30-40k, or according to experience)

Details on how to apply, link to application form and detailed job description at: http://tinyurl.com/myxa7ux
The website for isacommons.org can be found by clicking here. isacommons.org is registered through Easily.co.uk - get web site hosting or domain name registration here.
1
Add a comment...
 
Updated Segway 1.2 ontology entry in the #softwareontology. +Michael Hoffman , I've added all we discussed. I'm using "genome annotation" at the moment rather than "semi-automated genome annotation" - I'll add the latter once I've received an updated EDAM ontology from the EDAM folks - EDAM and SWO are merged, and that term is something more appropriate to their part of the hierarchy. Enjoy!
2
Melanie Courtot's profile photoAllyson Lister's profile photoStian Soiland-Reyes's profile photoJames Malone's profile photo
5 comments
 
+Stian Soiland-Reyes We will fix this in the New Year.
Add a comment...

Allyson Lister

Shared publicly  - 
 
Do you have what it takes? :)
 
SBML Editor nominations are now open! Submit your nominations by Dec. 8.
Drive
Nominating a new SBML Editor for 2015-2017This is a call for nominations for a new SBML Editor to replace one outgoing editor, Nicolas Le Novère, beginning in January 2015. The SBML Editor election process is described on the page at http://sbml.org/Documents/SBML_Development_Process/Election_of_SBML_Editors The SBML Editors play a key role in writing and developing SBML specifications. SBML Editors have to be willing to invest time and effort into evaluating proposals for changes, rese...
View original post
1
Add a comment...

Allyson Lister

Shared publicly  - 
 
 
Registration for HARMONY 2015 is open
The registration for HARMONY 2015 is now open. It will take place Mon. 20- Fri. 24 April 2015 at the Leucorea in Wittenberg, Germany.

HARMONY is a hackathon-type meeting, with a focus on development of the standards, interoperability and infrastructure. There are generally not many general discussions or oral presentations during HARMONY; instead, the time is devoted to allowing hands-on hacking and interaction between people focused on practical development of software and standards. 
View original post
1
Add a comment...
People
Have her in circles
7,881 people
Donald Tassie's profile photo
Bill Meade's profile photo
Brett Szmajda's profile photo
Justin Lundsteen's profile photo
Jari Sundell's profile photo
Rizal Rashid's profile photo
Alec Brownstein's profile photo
Dennis Humble's profile photo
David Mikulin's profile photo
Work
Occupation
Ontologist etc.
Skills
Biological data standards, semantic data, biological databases, ontologies
Employment
  • University of Oxford
    Knowledge Engineer, 2015 - present
    Development of the BioSharing.org project. http://www.biosharing.org
  • University of Manchester
    Ontologist, 2012 - 2014
    Part time work modifying the Software Ontology.
  • Newcastle University
    Research Asssociate, 2012 - 2014
  • Newcastle University
    PhD Student, 2006 - 2012
  • CISBAN, Newcastle University
    Research Associate, PhD Student, 2006 - 2011
  • European Bioinformatics Institute
    Senior Programmer, 1999 - 2006
Basic Information
Gender
Female
Story
Introduction
Interests include ontologies, data integration, data standards, systems biology, bioinformatics in general, and science news.

You can find more information about my research and my work interests at http://themindwobbles.wordpress.com

Help me to circle you correctly!
Education
  • Newcastle University
    Systems Biology / Computing Science, PhD, 2006 - 2012
  • University of York
    Biological Computation, MSc, 1998 - 1999
  • Rice University
    Biology / Ancient Mediterranean Civilizations, B.A., 1993 - 1997