Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature.
Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature.
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DOI：
10.1371/journal.pone.0010708
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发表时间：
2010-05-20
期刊：
影响因子：
3.7
通讯作者：
Mabee PM
中科院分区：
文献类型：
--
作者：
Dahdul WM;Balhoff JP;Engeman J;Grande T;Hilton EJ;Kothari C;Lapp H;Lundberg JG;Midford PE;Vision TJ;Westerfield M;Mabee PM
在已发表的系统发育系统学论文、专著和论文中记录的丰富的表型描述传统上是以自由文本格式报告的，因此很大程度上无法链接到遗传学、发育和表型的生物学数据库，并且难以管理以进行大规模的综合工作。Phenoscape项目旨在用丰富和形式化的语义来表示这些复杂和详细的描述，这些语义可以进行计算并与生物学其他领域的表型数据集成。这需要使用本体论将传统的自由文本字符重新概念化为可计算的实体质量(EQ)形式。我们使用了本体论和EQ形式论来收集47种骨藻鱼类(包括叉尾鱼、叉尾鱼、叉尾鱼)及其近亲的系统发育研究，目的是将这些复杂的表型描述与现有的模式生物数据库(斑马鱼，http://zfin.org).)中的信息相结合我们开发了一个收集这些出版物中的特征、分类和标本数据的管理工作流程。3,449个分类群(主要是物种)的4,617个表型特征(10,512个状态)被归类为EQ形式(总共12,861个EQ陈述)，使用来自特定于硬骨的本体(Teleost解剖学Ontology和Teleost Taxonomy Ontology)的解剖学和分类学术语以及来自质量本体(表型和特征Ontology)的术语。为了应对来自两个注释实验和来自馆长的反馈的明显挑战，制定了一致和准确地表示表型的标准和指南。我们遇到的挑战以及我们开发的许多用于提高一致性的管理标准和方法通常适用于使用本体表示表型的任何努力。这是因为，表型的详细变化的本体论表示，无论是在突变体或野生型之间，在个体人类之间，还是跨物种的多样性，都需要一个过程，通过这个过程，根据逻辑关系选择和组织来自领域本体的术语的精确组合。我们在这个过程中开发的效率将有助于任何使用本体论注释复杂表型描述的尝试。我们还讨论了EQ表示在系统学领域的一些分支。
The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage to biological databases for genetics, development, and phenotypes, and difficult to manage for large-scale integrative work. The Phenoscape project aims to represent these complex and detailed descriptions with rich and formal semantics that are amenable to computation and integration with phenotype data from other fields of biology. This entails reconceptualizing the traditional free-text characters into the computable Entity-Quality (EQ) formalism using ontologies. We used ontologies and the EQ formalism to curate a collection of 47 phylogenetic studies on ostariophysan fishes (including catfishes, characins, minnows, knifefishes) and their relatives with the goal of integrating these complex phenotype descriptions with information from an existing model organism database (zebrafish, http://zfin.org). We developed a curation workflow for the collection of character, taxonomic and specimen data from these publications. A total of 4,617 phenotypic characters (10,512 states) for 3,449 taxa, primarily species, were curated into EQ formalism (for a total of 12,861 EQ statements) using anatomical and taxonomic terms from teleost-specific ontologies (Teleost Anatomy Ontology and Teleost Taxonomy Ontology) in combination with terms from a quality ontology (Phenotype and Trait Ontology). Standards and guidelines for consistently and accurately representing phenotypes were developed in response to the challenges that were evident from two annotation experiments and from feedback from curators. The challenges we encountered and many of the curation standards and methods for improving consistency that we developed are generally applicable to any effort to represent phenotypes using ontologies. This is because an ontological representation of the detailed variations in phenotype, whether between mutant or wildtype, among individual humans, or across the diversity of species, requires a process by which a precise combination of terms from domain ontologies are selected and organized according to logical relations. The efficiencies that we have developed in this process will be useful for any attempt to annotate complex phenotypic descriptions using ontologies. We also discuss some ramifications of EQ representation for the domain of systematics.
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影响因子：
6.5
作者：
Dahdul WM;Lundberg JG;Midford PE;Balhoff JP;Lapp H;Vision TJ;Haendel MA;Westerfield M;Mabee PM
通讯作者：
Mabee PM
影响因子：
12.3
作者：
Gkoutos GV;Green EC;Mallon AM;Hancock JM;Davidson D
通讯作者：
Davidson D
DOI：
10.1111/j.1096-3642.2004.00109.x
发表时间：
2004-05-01
影响因子：
2.8
作者：
Armbruster, JW
通讯作者：
Armbruster, JW
DOI：
10.1111/j.1096-3642.2009.00550.x
发表时间：
2009-11-01
影响因子：
2.8
作者：
Clarke, Julia A.;Ksepka, Daniel T.;Norell, Mark A.
通讯作者：
Norell, Mark A.
DOI：
10.1111/j.1096-3642.2007.00306.x
发表时间：
2007-08-01
影响因子：
2.8
作者：
De Pinna, Mario C. C.;Ferraris, Carl J., Jr.;Vari, Richard P.
通讯作者：
Vari, Richard P.