Computable evolutionary phenotype knowledge: a hands-on workshop

 community, Informatics, Knowledge Base, knowledgebase, Outreach, Software, Workshops  Comments Off on Computable evolutionary phenotype knowledge: a hands-on workshop
Sep 302017
 

Call for Participation:

Computable evolutionary phenotype knowledge: a hands-on workshop

The Phenoscape project is hosting a hands-on workshop on Dec 11-14, 2017, at Duke University in Durham, North Carolina.

Evolutionary phenotype data that is amenable to computational data science, including computation-driven discovery, remains relatively new to science. Therefore use-cases and applications that effectively exploit these new capabilities are only beginning to emerge. If you are interested in discovering, linking to, recombining, or computing with machine-interpretable evolutionary phenotypes, this is the workshop for you!

The event will bring together a diverse group of people to collaboratively design and work hands-on on targets of their interest that take advantage and promote reuse of Phenoscape’s online evolutionary data resources and services. The event is designed as a hands-on unconference-style workshop. Participants will break into subgroups to collaboratively tackle self-selected
work targets.

The full Call for Participation, including motivation and scope, is posted here: https://hackmd.io/s/Sk6Xa7Eq-#

To apply to participate in the event, please fill out the application form by Oct 9, 2017. Travel sponsorship is available but limited, as is space.


Filed under: Informatics, Knowledge Base, Outreach, Workshops Tagged: community, knowledgebase, Software, Workshops

Report from Tucson: from characters to annotations with text mining

 Data Curation, NLP, Phenex, Software  Comments Off on Report from Tucson: from characters to annotations with text mining
Mar 302013
 

There is a wealth of phenotypic information in the evolutionary literature that comes in the the form of semi-structured character state descriptions. To get that information into computable form is, right now, an awfully slow process. In Phenoscape I, we estimated that it took about five person-years in total to curate semantic phenotype anphenowordcloudnotations from 47 papers. If we are to get computable evolutionary phenotypes from a larger slice of the literature, we really need to figure out ways to speed this up.

One promising approach is to use text-mining.  This could contribute in a few different ways.  First, one could efficiently identify all the terms in the text that are not currently represented in ontologies and add them en masse, so that data curation does not have to stop and resume whenever such terms are encountered. Second, one could present a human curator with suggestions for what terms to use and what relations those terms have to one another, speeding the process of composing an annotation.

CharaParser, developed by Hong Cui at the University of Arizona, is an expert-based system that decomposes character descriptions into recognizable grammatical components, and it is now being used in several different biodiversity informatics projects. Baseline evaluation results from BioCreative III showed that a naive workflow combining CharaParser and Phenex, the software curators use to compose ontological annotations and relate them to character states, was capable of identifying candidate entity and quality phrases (it outperformed biocurators by 20% in recall on average) but had difficulty translating those into ontological annotations.  This first iteration workflow also was not yet reducing curation time.

In March, a small contingent from NESCent (Jim Balhoff, Hilmar Lapp and Todd Vision) visited Hong Cui’s group in Tucson. We talked through improvements to CharaParser and the curation workflow, brainstormed plans for a more thorough set of evaluation tests, began refactoring of the code so that it can be more easily shared across projects, and gained a better understanding of what features make a character difficult to curate for humans vs. text-mining.  We made substantial progress on all fronts, and are looking forward to seeing how much improvement in the accuracy and efficiency of curation will be achieved in the next round of testing.

We are also pleased to report that the CharaParser codebase will now be available from GitHub under an open source (MIT) license.


Filed under: Data Curation, NLP, Ontology, Phenex, Software

Phenoscape goes mobile

 Knowledge Base, Software  Comments Off on Phenoscape goes mobile
Jul 092012
 

Previous layout of the KB faceted browsing page on the iPhone. Text is tiny and must be zoomed and panned.

The NESCent Informatics group periodically holds “hack days”, one day mini-hackathons where we take a break from our usual schedule and push forward on a specific topic of interest. Most recently, the topic was support for the mobile web. I took a look at the Phenoscape Knowledgebase layout on the iPad and iPhone. In general the site did not adapt well to small screen sizes.

In order to avoid serving different layouts to specific devices, I applied techniques from the Responsive Web Design approach, which uses new functionality from CSS 3 to dynamically adjust the page layout based on the size of the browser window. In the new layout, when the window is small, controls move from the side to the top, allowing both the controls and the content table to use the full screen width.

Using responsive web design, the controls and content become stacked on small screens.

The new layout works across most of the pages on the Knowledgebase site. In general, it is a big improvement on mobile devices. However, there are a few remaining glitches to address, such as controls that appear upon mouse hover: difficult to use on a touchscreen device, where there is no mouse.


Filed under: Knowledge Base, Software
 Posted by on July 9, 2012 at 9:00 pm  Tagged with:
Mar 012012
 

On the last day of a very successful Phenotype RCN meeting at Nescent last week , we held an impromptu session on OBO to OWL mappings.  This was based on the a recent workshop run for GO curators by myself (David Osumi-Sutherland), Chris Mungall,  Simon Jupp and Jane Lomax.  By popular demand, I’ve posted my slides on slideshare.

The original workshop also included an intro to Protégé 4 by Simon Jupp [warning: word doc] as well as a set of problem solving exercises consisting of a set of folders each featuring one or more test ontologies and a README with instructions. For best results, you should checkout the whole repository of exercises using an svn client: svn checkout http://oboformat.googlecode.com/svn/docs/tutorial/ obo2owl_tut_read_only
Details of the software required for these exercises can be found at http://tinyurl.com/86w9xud

Third beta release of Phenoscape Knowledgebase 2.0

 Development, Knowledge Base, Software  Comments Off on Third beta release of Phenoscape Knowledgebase 2.0
Feb 072011
 

Phenoscape Knowledgebase 2.0 beta release 3 is now available at http://kb.phenoscape.org/. This version includes an enhanced publication info interface [example] which displays the original character matrix, as well as a list of taxa including the taxonomic names and museum specimens used in the dataset. Other recent developments in the KB are global term info popups and hierarchical browsing of ontology terms on their info pages [example].

We have also improved our software and data release processes so that the public Knowledgebase can easily keep up with new developments and the latest data updates from our curators. Looking forward, the next major feature to be added to the Knowledgebase is a faceted browsing interface which is currently under development. This interface should help provide an overview of how the data are organized within the various ontologies used in the Knowledgebase.


Filed under: Development, Knowledge Base, Software
 Posted by on February 7, 2011 at 6:15 pm  Tagged with:

Revising the Knowledgebase interface

 Development, Knowledge Base, Software  Comments Off on Revising the Knowledgebase interface
Mar 242010
 

We have been developing mockup versions of new web interfaces for the Phenoscape Knowledgebase.  In order to design an updated interface which is both more powerful and easier to use than the existing one, in February I presented a series of mockups to faculty, post-docs, and graduate students at the University of Oregon, the home of ZFIN.  Following user-testing expertise at ZFIN, I met with the researchers in pairs and recorded their feedback on newly designed interfaces for viewing anatomical and taxonomic terms within the ontology hierarchy, configurable queries for phenotype annotations, and data visualization on phylogenetic trees.  The feedback proved to be extremely valuable and has led to several modifications to the planned interface revisions.


Filed under: Development, Knowledge Base, Software
 Posted by on March 24, 2010 at 4:54 pm  Tagged with:

Phenex 1.0.3 released

 Curation Tools, Informatics, Phenex, Software  Comments Off on Phenex 1.0.3 released
Feb 232010
 

Phenex 1.0.3 is now available.  This release fixes a serious bug which caused Phenex to append modified phenotype annotations within files, instead of replacing the previous data. Phenex will now read and write NeXML files correctly. It should also automatically recover the latest data from files saved with older versions of Phenex.

All Phenex users should replace their current copy of Phenex with the latest release. It can be downloaded from the Phenex homepage on the Phenoscape wiki.


Filed under: Curation Tools, Informatics, Phenex, Software
 Posted by on February 23, 2010 at 9:14 pm  Tagged with: