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Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient

Arlin Stoltzfus, Hilmar Lapp, Naim Matasci, Helena Deus, Brian Sidlauskas, Christian M Zmasek, Gaurav Vaidya, Enrico Pontelli, Karen Cranston, Rutger Vos, Campbell O Webb, Luke J Harmon (+16 others)
2013 BMC Bioinformatics  
Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great "Tree of Life" (ToL).  ...  While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form.  ...  Such a system will not replace the time-consuming generation of robust phylogenies by experts, but aims to make those hard-won results conveniently accessible to everyone else.  ... 
doi:10.1186/1471-2105-14-158 pmid:23668630 pmcid:PMC3669619 fatcat:5gj4e7u4vjbkrcbrappwoqq3aq

The Shape of Trees – Limits of Current Diversification Models [article]

Orlando Schwery, Brian C. O'Meara
2021 bioRxiv   pre-print
Patterns of adequacy are described across trees and models and causes for inadequacy – particularly if all models are inadequate – are explored.  ...  Using a large set of empirical phylogenies, and a new approach to test models using aspects of tree shape, we test how a set of staple models performs with regards to adequacy.  ...  . & Jordan, G. (2013) Phylotastic! Making tree-of-life knowledge accessible, 407 reusable and convenient.  ... 
doi:10.1101/2021.01.26.428344 fatcat:dif5ldr6f5gsfbb7mlcpoeni6u

BioHackathon 2015: Semantics of data for life sciences and reproducible research

Rutger A. Vos, Toshiaki Katayama, Hiroyuki Mishima, Shin Kawano, Shuichi Kawashima, Jin-Dong Kim, Yuki Moriya, Toshiaki Tokimatsu, Atsuko Yamaguchi, Yasunori Yamamoto, Hongyan Wu, Peter Amstutz (+65 others)
2020 F1000Research  
the reusability of biological data.  ...  We discuss issues surrounding the representation, publication, integration, mining and reuse of biological data and metadata across a wide range of biomedical data types of relevance for the life sciences  ...  ) and the Database Center for Life Science (DBCLS).  ... 
doi:10.12688/f1000research.18236.1 pmid:32308977 pmcid:PMC7141167 fatcat:oaglnztjrrhpvgluujl3reudoe

Patent Conflicts in User-Driven Biotechnology: Examining Knowledge Management Strategies for Patentable Research Resources to Stimulate DIY Bio and Other Social Production in Biotechnology

Haewon Chung, University, My
The proliferation of patents and related rights protecting upstream research can be detrimental to progress and citizens' welfare because they can increase the cost of R&D, interfere with access to upstream  ...  Many DIYers depend on self-funding and community resources to experiment with biotechnology. Proprietary research tools and equipment are harder to access.  ...  Making tree-of-life knowledge accessible, reusable, and convenient" (2013), 14 BMC Bioinformatics 158); Peter B Nichol "Hacking the future of health at Yale", CIO Magazine (26 January 2017) online: CIO  ... 
doi:10.20381/ruor-25839 fatcat:jshlqcc7gzbpzjzhhaa6aibgle

OASIcs, Volume 64, ICLP'18, Complete Volume [article]

Alessandro Dal Palu', Paul Tarau, Neda Saeedloei, Paul Fodor
The availability of efficient answer set solvers (e.g., clasp and its descendants [8, 2]) gave Answer set programming (ASP) a leading role in languages for knowledge representation and reasoning.  ...  ASP is regarded as the computational embodiment of non-monotonic reasoning because of its simple syntax and elegant non-monotonic semantics.  ...  Introduction The Phylotastic 1 project is an attempt for making use of phylogeny trees in education or for researching in biology.  ... 
doi:10.4230/oasics.iclp.2018 fatcat:exbunzcx7rgrhg32iguyfxca7u