The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.
The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.
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DOI：
10.1186/s13326-016-0097-6
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发表时间：
2016-09-23
影响因子：
1.9
通讯作者：
Mungall CJ
中科院分区：
文献类型：
--
作者：
Buttigieg PL;Pafilis E;Lewis SE;Schildhauer MP;Walls RL;Mungall CJ
2013年首次描述的环境本体（ENVO; http：//www.environmentontology.org/）是用于环境实体的语义控制描述的资源和研究目标。本体论的最初目标是表示与基因组和微生物组相关的研究有关的生物群系、环境特征和环境材料。然而，对环境语义学的需求在许多领域都是共同的，ENVO的使用自其最初的描述以来一直在稳步增长。因此，我们已经扩大，增强和推广的本体，以支持其日益多样化的应用。我们已经更新了我们的开发套件，以提高表现力，一致性和速度：我们现在使用Web本体语言（OWL）开发ENVO，并采用模板方法来加速类创建。我们还采取措施，使ENVO更好地与开放生物和生物医学本体（OBO）Foundry原则保持一致，并与现有的OBO本体进行互操作。此外，我们应用文本挖掘方法从生命百科全书中提取栖息地信息，并在ENVO中自动创建实验栖息地类。相对于2013年的状态，ENVO的内容，范围和实施都得到了增强，其现有内容的大部分都经过了修改，以改进语义表示。ENVO现在提供栖息地，环境过程，人为环境以及与环境健康倡议和全球2030年可持续发展议程相关的实体的代表。ENVO的几个分支已被用于在以前未代表的领域（如食品和农学）中孵化和播种新的本体。OWL格式的本体的当前发布版本可在http://purl.obolibrary.org/obo/envo.owl上获得。ENVO已经形成了一个本体论，它连接了多个领域，包括生物医学，自然和人类生态学，“组学”和社会经济发展。通过与我们的用户和合作伙伴的持续互动，特别是那些执行数据归档和合成的用户和合作伙伴，我们预计ENVO的增长将在2017年加速。与往常一样，我们邀请进一步的贡献和合作，以推进环境的语义表示，从地理特征和环境材料，跨越栖息地和生态系统，到家庭环境中的日常物品。
The Environment Ontology (ENVO; http://www.environmentontology.org/), first described in 2013, is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. However, the need for environmental semantics is common to a multitude of fields, and ENVO's use has steadily grown since its initial description. We have thus expanded, enhanced, and generalised the ontology to support its increasingly diverse applications. We have updated our development suite to promote expressivity, consistency, and speed: we now develop ENVO in the Web Ontology Language (OWL) and employ templating methods to accelerate class creation. We have also taken steps to better align ENVO with the Open Biological and Biomedical Ontologies (OBO) Foundry principles and interoperate with existing OBO ontologies. Further, we applied text-mining approaches to extract habitat information from the Encyclopedia of Life and automatically create experimental habitat classes within ENVO. Relative to its state in 2013, ENVO's content, scope, and implementation have been enhanced and much of its existing content revised for improved semantic representation. ENVO now offers representations of habitats, environmental processes, anthropogenic environments, and entities relevant to environmental health initiatives and the global Sustainable Development Agenda for 2030. Several branches of ENVO have been used to incubate and seed new ontologies in previously unrepresented domains such as food and agronomy. The current release version of the ontology, in OWL format, is available at http://purl.obolibrary.org/obo/envo.owl. ENVO has been shaped into an ontology which bridges multiple domains including biomedicine, natural and anthropogenic ecology, ‘omics, and socioeconomic development. Through continued interactions with our users and partners, particularly those performing data archiving and sythesis, we anticipate that ENVO’s growth will accelerate in 2017. As always, we invite further contributions and collaboration to advance the semantic representation of the environment, ranging from geographic features and environmental materials, across habitats and ecosystems, to everyday objects in household settings.
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影响因子：
1.9
作者：
Buttigieg PL;Morrison N;Smith B;Mungall CJ;Lewis SE;ENVO Consortium
通讯作者：
ENVO Consortium
影响因子：
--
作者：
Deck, John;Barker, Katharine;Wooley, John
通讯作者：
Wooley, John
影响因子：
10.3
作者：
Ellis, Erle C.;Ramankutty, Navin
通讯作者：
Ramankutty, Navin
影响因子：
3.7
作者：
Flores GE;Bates ST;Knights D;Lauber CL;Stombaugh J;Knight R;Fierer N
通讯作者：
Fierer N
影响因子：
3.7
作者：
Dunn RR;Fierer N;Henley JB;Leff JW;Menninger HL
通讯作者：
Menninger HL