Fwd: iEvoBio submission: Accepted

[Hilmar Lapp]

FYI, a group of us submitted a lightning talk on the MIAPA ontology to the iEvoBio conference. The submission has now been accepted. I'm attaching the abstract for those interested.

-hilmar


Begin forwarded message:

> From: iEvoBio 2013 <karen.c...@nescent.org>
> Subject: iEvoBio submission: Accepted
> Date: June 3, 2013 9:23:34 AM EDT
> To: hl...@nescent.org
> Reply-To: karen.c...@nescent.org
>
> Dear Hilmar,
> On behalf of the iEvoBio organizing committee, I am happy to accept your submission The MIAPA ontology: An annotation ontology for validating minimum metadata reporting for phylogenetic analyses to iEvoBio. Here are a couple of notes about the various types of submissions:
>
> If you are giving a lightning talk, we encourage you to use auto-advancing slides (in the style of Ignite, http://en.wikipedia.org/wiki/Ignite_(event)). If you are also presenting in the software bazaar, your talk will serve as the introduction to your software demo.
>
> If you are participating in the software bazaar and NOT giving a lightning talk, we will start the bazaar with very brief introductions to each software package. Please prepare 2 introductory slides (PDF format). We will collect these during the first day of the conference.
>
> We look forward to seeing you in Snowbird!
>
> Sincerely,
> Karen Cranston
> iEvoBio organizing committee
>

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: Hilmar Lapp -:- Durham, NC -:- informatics.nescent.org :
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[Hilmar Lapp]

I should have added that a poster submission to the 2013 ISMB conference with a similar abstract and a nearly identical group of co-authors has also been accepted. I'm pasting in the abstract below; one of the main differences to the iEvoBio submission (aside from poster vs talk) is that the data integration part is not included here (which is why Joachim isn't a co-author on this one).

-hilmar

An annotation ontology for validating minimum metadata reporting for phylogenetic analyses

Determining a published phylogenetic tree’s fitness for reuse towards some purpose depends on the availability of certain metadata, such as the type of alignment from which it was constructed, the method used to infer it, or whether branch lengths are present. This principle motivated the Minimum Information About a Phylogenetic Analysis (MIAPA) metadata reporting standard, first articulated in 2006 by Leebens-Mack et al. While many alignment and phylogenetic inference programs output some metadata suggested by the MIAPA vision, a formal definition of what is required or recommended is still lacking, and there is no commonly followed vocabulary convention that tools and users could rely on for extracting MIAPA-relevant information from a phylogenetic tree under consideration. To address this gap, we created the MIAPA ontology, an application ontology designed for annotating phylogenetic data. The ontology is developed in OWL, and reuses concepts from several existing ontologies, including the Comparative Data Analysis Ontology (CDAO), the Information Artifact Ontology (IAO), the Software Ontology (SWO and EDAM), and the W3C Provenance Ontology (PROV). The ontology aims to implement the recommendations made by an informal draft consensus checklist. Using previously published trees, we give examples for using the ontology, and we present the challenges in translating informal, sometimes ambiguous checklist recommendations into formal ontologies. We also consider the potential of formalizing a minimum metadata reporting standard as an ontology for enabling data sharing platforms to assess, rate, and thereby incentivize metadata quality and richness of their data contents for the benefit of their users.

> <MIAPAontology-iEvoBio2013abstract.pdf>