The 1994 CBE (Council of Biology Editors) manual, Scientific Style and Format, describes two systems of documentation, the citation-sequence system and the name-year system. This handout provides guidelines for each system. (For a class paper, check to see if your instructor prefers one of these systems or another. For a journal article, check the journal's instructions to authors to find out which system to use.) The CBE manual specifies that journal titles should be abbreviated, and it provides rules for abbreviation and a list of standard abbreviations of words commonly used in titles. Although this handout focuses on documentation style, you should be aware that the manual also contains information on many other aspects of scientific style, from prose style to handling of numbers, tables and figures, and conventions in a variety of scientific areas. ... [Information of the supplier]
The Global Names Architecture (GNA) is a system of databases, programs, and web services - a cyberinfrastructure - that can be used to discover, index, organize and interconnect on-line information about organisms and their names. When a thing has a name, that name becomes an anchor around which we can collect our observations and knowledge. The use of names as a framework for knowledge of biology began with the system of scientific names introduced by Linnaeus about 250 years ago. His approach was to use latin binomials, such as Ba humbugi (it's a snail), Pompholyxophrys punicea (a microbe) or Homo sapiens (a self-aware biped). This system is still used for almost all organisms. Names are included in almost every statement and database about organisms. In the e-world, names are metadata which can be used to discover and organize information about organisms. The Global Names Architecture is a communal open environment that manages names so that we can manage information about organisms and serve the needs of biologists. ... [Information of the supplier]
Ecological Metadata Language (EML) is a metadata specification developed by the ecology discipline and for the ecology discipline. It is based on prior work done by the Ecological Society of America and associated efforts (Michener et al., 1997, Ecological Applications). EML is implemented as a series of XML document types that can by used in a modular and extensible manner to document ecological data. Each EML module is designed to describe one logical part of the total metadata that should be included with any ecological dataset. The EML project is an open source, community oriented project dedicated to providing a high-quality metadata specification for describing data relevant to the ecological discipline. The project is completely comprised of voluntary project members who donate their time and experience in order to advance information management for ecology. Project decisions are made by consensus according to the voting procedures described in the ecoinformatics.org Charter. ... [Information of the supplier]
The OBO Foundry is a collaborative experiment involving developers of science-based ontologies who are establishing a set of principles for ontology development with the goal of creating a suite of orthogonal interoperable reference ontologies in the biomedical domain. The groups developing ontologies who have expressed an interest in this goal are listed below, followed by other relevant efforts in this domain. In addition to a listing of OBO ontologies, this site also provides a statement of the OBO Foundry principles, discussion fora, technical infrastructure, and other services to facilitate ontology development. ... [Information of the supplier]
The intention of the GoldenGATE editor is to build a bridge between NLP components and XML markup of natural language text according to arbitrary XML schemas. It allows the deployment of NLP components to marking up the bodies of literature they were designed for. In this way, it enables transforming the texts into XML content according to an XML schema that was designed to gain maximum benefit from the knowledge provided in them. The GoldenGATE editor picks up the ideas of plug-in processing resources and pipelined processing implemented in the GATE framework (http://www.gate.co.uk), which has been widely used in many areas of NLP research. At the same time, it provides a full XML editor including assistance for manipulation of both text and markup, thus allowing users to improve data quality by manual intervention. In order to achieve maximum flexibility and extensibility, the GoldenGATE editor provides plug-and-play interfaces on many levels: Individual automated components for markup creation and manipulation, entire groups of functionalities, components accessing documents in arbitrary storage locations, and arbitrary document data formats. ... [Information of the supplier]
This is the home page of the Fungal Anatomy Ontology project. The project aims to develop a controlled vocabulary to describe the 'anatomy' of fungi and other microbes, called the fungal anatomy ontology (FAO). The ontology has been deposited with the Open Biomedical Ontologies (OBO). The FAO ontology is orthogonal to those developed by the GO Consortium and the others listed at the OBO. Thus, the FAO may be used alone or in conjunction with the ontologies at GO and OBO to make robust functional annotations. Researchers are encouraged to help develop and to use the FAO in their work. ... [Information of the supplier]
The Environment Ontology (EnvO) provides a controlled, structured vocabulary that is designed to support the annotation of any organism or biological sample with environment descriptors. EnvO contains terms for biomes, environmental features, and environmental material. Examples of biome terms are: boreal moist forest biome, tropical rain forest biome, and oceanic pelagic zone biome. Examples of environmental feature terms are: mountain, pond, whale fall, and karst. Examples of environmental material terms are: sediment, soil, water, and air These three sets of terms enable a concise, standardised, and comprehensive description of environment that is key to the integration, archiving and federated searching of environmental data. As a tool for the life sciences, we see EnvO bringing similar benefits to the Gene Ontology (GO). Through promoting consistent annotation grounded in an ontological framework, we hope to facilitate the semantic retrieval of any biological record anchored to EnvO. Records contained in sequence databases, omic data repositories, tissue banks and museum collections are prime candidates for EnvO annotation.However, EnvO is also suitable for the annotation of any record that has an environmental component. For example, you can use EnvO terms to provide information on the environment of remote sensing devices or simply to tag a picture that you took at the weekend. Further, the EnvO project is closely tied with GAZ, a first step towards an open source gazetteer constructed on ontological principles. GAZ describes places and place names as well as the relations between them and, when linked with EnvO descriptors, provides a basis to infer environment from place names. ... [Information of the supplier]
GONUTS is a Gene Ontology Normal Usage Tracking System. The GONUTS wiki has been set up to provide third-party documentation for users of the Gene Ontology Project. The GO wiki is not an official product of the GO consortium. It was built by users at TAMU for newcomers to GO who want to explore GO usage. The rationale for this wiki is described in "About GONUTS". To enter the ontology pages, go to the GO page, or search for a term. For more information about how this wiki is automatically updated, see GO wiki scripts. For Help using the system, see Help: Contents, which is available in the navigation links from all pages. See Current events for what's new with the GONUTS wiki. Leave comments and suggestions on our Known Issues page. ... [Information of the supplier]
If two different species, genera or other taxons have the same name, this name is a homonym. Homonyms are illegal if they belong to the same code of nomenclature. If same name belongs to different codes, it is a hemihomonym (Starobogatov, 1991). Despite of their validity, hemihomonyms are misleading and even dangerous. If there is a possibility that a name is a hemihomonym, use postfix (b), (c) or (z) for names covered by Botanical, Bacteriological, or Zoological codes of nomenclature, respectively. To check if name is a hemihomonym, please use table below or the query with this search API prototype. ... [Information of the supplier]