Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.
Phylotastic! Making tree-of-life knowledge accessible, reusable and convenient.
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系统！使生活树知识可访问，可重复和方便。
DOI：
10.1186/1471-2105-14-158
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发表时间：
2013-05-13
影响因子：
3
通讯作者：
Jordan G
中科院分区：
文献类型：
--
作者：
Stoltzfus A;Lapp H;Matasci N;Deus H;Sidlauskas B;Zmasek CM;Vaidya G;Pontelli E;Cranston K;Vos R;Webb CO;Harmon LJ;Pirrung M;O'Meara B;Pennell MW;Mirarab S;Rosenberg MS;Balhoff JP;Bik HM;Heath TA;Midford PE;Brown JW;McTavish EJ;Sukumaran J;Westneat M;Alfaro ME;Steele A;Jordan G
科学家们很少重复使用关于生命发生的专业知识，尽管他们多年来一直在努力组装一棵伟大的“生命之树”（ToL）。一个值得注意的例外涉及Phylomatic的使用，它提供了从大型的、预先计算的、专家级的植物分类群生成自定义分类群的工具。这表明一个更广义的系统，从一个查询组成的任何已知的物种的列表，将纠正非标准的名称，确定专家包含牵连的类群，修剪掉不需要的部分，并提供分支长度和注释，从而在一个自定义的系统适合用户的需要，具有很大的潜力。这样的系统可以成为一个可持续的社区资源，如果实现为一个松散耦合的部分，通过明确定义的接口进行交互的分布式系统。为了建立这样一个“系统分类”的系统，NESCent黑客松，互操作性，系统发育（HIP）工作组在2012年6月招募了24名科学家程序员参加为期一周的编程黑客活动。在黑客攻击期间，（以及三个月的随访期），5个团队进行了设计、实现、文档、演示和测试，包括：（1）集成组件的通用方案;（2）概念验证修剪器和控制器;（3）元API用于分类名称解析服务;（4）使用语义网技术进行数据交换、存储和查询，用于存储、查找和检索数据生成的系统;（5）创新的新服务DateLife.org，其综合预先计算的、时间校准的数据生成，以分配节点的年龄;以及（6）示范项目。这些结果可以通过公共代码库（GitHub.com）、网站（http：//www.example.com）和服务器映像访问。www.phylotastic.org大约9个人工月的努力（以软件开发黑客为中心）为4个核心系统组件、3个控制器和3个最终用户演示工具设计和实施了概念验证软件。虽然这些产品有很大的局限性，他们提出了相当大的潜力，分布式系统，使系统发育的知识容易获得可计算的形式。系统分类系统的广泛使用将创建一个共享系统分类知识的电子市场，这将刺激ToL企业其他领域的创新，例如来源和方法的注释以及质量评估的第三方方法。
Scientists rarely reuse expert knowledge of phylogeny, in spite of years of effort to assemble a great “Tree of Life” (ToL). A notable exception involves the use of Phylomatic, which provides tools to generate custom phylogenies from a large, pre-computed, expert phylogeny of plant taxa. This suggests great potential for a more generalized system that, starting with a query consisting of a list of any known species, would rectify non-standard names, identify expert phylogenies containing the implicated taxa, prune away unneeded parts, and supply branch lengths and annotations, resulting in a custom phylogeny suited to the user’s needs. Such a system could become a sustainable community resource if implemented as a distributed system of loosely coupled parts that interact through clearly defined interfaces. With the aim of building such a “phylotastic” system, the NESCent Hackathons, Interoperability, Phylogenies (HIP) working group recruited 2 dozen scientist-programmers to a weeklong programming hackathon in June 2012. During the hackathon (and a three-month follow-up period), 5 teams produced designs, implementations, documentation, presentations, and tests including: (1) a generalized scheme for integrating components; (2) proof-of-concept pruners and controllers; (3) a meta-API for taxonomic name resolution services; (4) a system for storing, finding, and retrieving phylogenies using semantic web technologies for data exchange, storage, and querying; (5) an innovative new service, DateLife.org, which synthesizes pre-computed, time-calibrated phylogenies to assign ages to nodes; and (6) demonstration projects. These outcomes are accessible via a public code repository (GitHub.com), a website (http://www.phylotastic.org), and a server image. Approximately 9 person-months of effort (centered on a software development hackathon) resulted in the design and implementation of proof-of-concept software for 4 core phylotastic components, 3 controllers, and 3 end-user demonstration tools. While these products have substantial limitations, they suggest considerable potential for a distributed system that makes phylogenetic knowledge readily accessible in computable form. Widespread use of phylotastic systems will create an electronic marketplace for sharing phylogenetic knowledge that will spur innovation in other areas of the ToL enterprise, such as annotation of sources and methods and third-party methods of quality assessment.
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影响因子：
3.3
作者：
Leebens-Mack, Jim;Vision, Todd;Zmasek, Christian
通讯作者：
Zmasek, Christian
影响因子：
5.8
作者：
Lewis, PO
通讯作者：
Lewis, PO
影响因子：
3
作者：
Boyle B;Hopkins N;Lu Z;Raygoza Garay JA;Mozzherin D;Rees T;Matasci N;Narro ML;Piel WH;McKay SJ;Lowry S;Freeland C;Peet RK;Enquist BJ
通讯作者：
Enquist BJ
影响因子：
3
作者：
Han MV;Zmasek CM
通讯作者：
Zmasek CM
DOI：
10.1073/pnas.0508430102
发表时间：
2005-11-29
影响因子：
11.1
作者：
Farris, SM;Roberts, NS
通讯作者：
Roberts, NS