Raptor Search Sources

USGS Websites and Databases:

Select biological content from the USGS, including Science Center research, NBII web pages, and catalogs supported by the NBII.

Ecosystems

The USGS Ecosystems mission area provides content related to freshwater, terrestrial, and marine ecosystems and the human, fish, and wildlife communities they support.

NBII FGDC Metadata Clearinghouse

The NBII's Metadata Clearinghouse provides citations describing and linking to geographically-referenced content, presented in the required format of the Federal Geographic Data Committee (FGDC).

NBII LIFE

The NBII's Library of Images for the Environment (LIFE) contains well-documented images of nature contributed by individuals and organizations. The photographic collections cover a wide breadth of topics, including images of plants, animals, fungi, microorganisms, habitats, wildlife management, environmental topics, and biological study/fieldwork.

NBII Web

Public content of the National Biological Information Infrastructure (NBII) site, including geographic and thematic sections of the NBII.

USGS Newsroom

News releases about USGS activities issued by the Office of Communications.

USGS Publications Warehouse

Public content of the National Biological Information Infrastructure (NBII) site, including geographic and thematic sections of the NBII.

Science Centers

Alaska Science Center (ASC)

Selected content from the USGS Alaska Science Center covering fish and fisheries, mammals, birds, ecosystems and habitats, and technical programs.

Columbia Environmental Research Center (CERC)

The USGS Columbia Environmental Research Center provides research project descriptions addressing topics such as national and international environmental contaminant issues and effects of habitat alterations on aquatic and terrestrial ecosystems.

Forest and Rangeland Ecosystem Science Center (FRESC)

The USGS Forest and Rangeland Ecosystem Science Center performs research in support of sound management and conservation of biological systems in the western United States.

Fort Collins Science Center (FCSC)

The USGS Fort Collins Science Center provides science-based information and tools needed for understanding the Nation's biological resources in support of effective decision making.

Great Lakes Science Center (GLSC)

The USGS Great Lakes Science Center provides information on living resources and their habitats in the Great Lakes basin ecosystem.

Leetown Science Center (LSC)

The USGS Leetown Science Center performs research on aquatic and terrestrial organisms and their supporting ecosystems.

National Wetlands Research Center (NWRC)

The USGS National Wetlands Research Center provides scientific information for managing and restoring wetland habitats and associated plant and animal communities.

National Wildlife Health Center (NWHC)

The USGS National Wildlife Health Center provides content gathered to support science-based decisions affecting wildlife and ecosystem health.

Northern Prairie Wildlife Research Center (NPWRC)

The Northern Prairie Wildlife Research Center provides scientific information needed to conserve and manage the nation's biological resources, with an emphasis on the species and ecosystems of the nation's interior.

Northern Rocky Mountain Science Center (NOROCK)

The USGS Northern Rocky Mountain Science Center provides scientific information for managing and restoring the ecosystems and associated plant and animal communities of the Northern Rockies.

Pacific Island Ecosystem Research Center (PIERC)

The USGS Pacific Island Ecosystems Research Center performs research on biological resources occurring in Hawaii`i and other Pacific island locations.

Patuxent Wildlife Research Center (PWRC)

The USGS Patuxent Wildlife Research Center performs wildlife and applied environmental research, with an emphasis on natural resource conservation.

Southeast Ecological Science Center (SESC)

The USGS Southeast Ecological Science Center performs research on amphibians and reptiles, coastal and benthic ecology, freshwater fauna, contaminants and ecotoxicology, imperiled fish, manatees, and invasive species of the southeast.

Southwest Biological Science Center (SBSC)

The Southwest Biological Science Center has research on water use, wildland fires, environmental contaminants and a variety of livestock and wildlife issues.

Upper Midwest Environmental Sciences Center (UMESC)

The USGS Upper Midwest Environmental Sciences Center performs research focused on river ecology, restoration of degraded habitats, declining species, invasive species, decision support model development (DSS), and the ecosystems of the Mississippi River Basin and the Great Lakes Basin.

Western Ecological Research Center (WERC)

The USGS Western Ecological Research Center provides research project descriptions addressing the management of Pacific Southwestern ecosystems.

Western Fisheries Research Center (WFRC)

The USGS Western Fisheries Research Center performs research focused on environmental factors affecting fish populations and their interactions in aquatic communities and ecosystems in the West.

 

Related Sites:

Web sites offered by governments, non profits, educational institutions, and more, selected for their coverage of biodiversity issues.

Biodiversity Heritage Library

The Biodiversity Heritage Library is a collection of the historical literature on biodiversity, in digitized form.

BioOne

The BioOne collection provides peer-reviewed research in the biological, ecological, and environmental sciences [Includes citations and full text].

ConserveOnline

Content from ConserveOnline, the Nature Conservancy's Web-based library on conservation of natural resources.

Cornell Ornithology Lab Birds of North America Online: Species List

The Cornell Ornithology Lab Birds of North America Online: Species List provides species profiles and summary information for North American birds.

DEPT. OF DEFENSE THREATENED AND ENDANGERED SPECIES DOCUMENT REPOSITORY

The Dept. of Defense Threatened and Endangered Species Document Repository provides reports on animal species that are threatened, endangered, or otherwise challenged on U.S. military reservations.

Fire Research And Management Exchange System

The Fire Research and Management Exchange System is a database resource that makes available data, documents, and tools for solving wildland fire problems.

GBIF (Global Biodiversity Information Facility)

Content from the Global Biodiversity Information Facility (GBIF), an international collection of data and documents on biodiversity and the life sciences.

International Union for Conservation of Nature (IUCN) Redlist

The International Union for Conservation of Nature (IUCN) Redlist provides species profiles and accounts for animal species that are threatened, endangered or otherwise challenged.

Invasive Plant Atlas of New England

The Invasive Plant Atlas of New England is a comprehensive web-accessible database of invasive and potentially invasive plants in New England, continually updated.

National Park Service

Selected content from the National Park Service, tasked with protecting our nation's heritage.

NBII Web Resources Database

The NBII's Web Resources Database contains selected Web content hand-picked by NBII staff for relevance to biodiversity issues.

NOAA: National Marine Fisheries Service

NOAA's National Marine Fisheries Service provides content relevant to the stewardship of living marine resources.

Pew Center on Global Climate Change

The Pew Center on Global Climate Change provides reports, briefs, policy analyses, and working papers on topics related to climate change.

State Wildlife Action Plans

The State Wildlife Action Plans assess the health of each state's wildlife and habitats, identify the problems they face, and outline the actions that are needed to conserve them over the long term.

U.S. Fish and Wildlife Service

Selected content from the U.S. Fish and Wildlife Service web collections, covering topics in fish and wildlife management.

U.S. Forest Service: Treesearch

Citations, with links to full-text, from Treesearch, a U.S. Forest Service database of forestry articles and research reports.

Additional Sources (Federated Search):

Optional federated searching of several large specialized databases. Use Advanced Search or the Sources tab on the search results page to access these additional sources.

Avibase

Avibase is an extensive database information system providing taxonomic and distribution information on bird species of the world.

Amphibiaweb

Amphibiaweb contains information on amphibian declines, conservation, natural history, and taxonomy.

GPOPubs

GPOPubs makes available citations from the Government Printing Office's online Catalog of U.S. Government Publications database.

NDLTD

Theses and dissertations of academic institutions worldwide, from the Networked Digital Library of Theses and Dissertations (NDLTD).

NEPIS

Citations from the Environmental Protection Agency's National Environment Publications Internet Site (NEPIS) database.

TROPICOS

Tropicos provides content from a botanical database organizing millions of plant specimens, images, and bibliographic references.

Starting Your Search

There are three ways to start a search:

• Simple search - type a keyword or a combination of keywords into a search box, located at the top right corner of every page of the NBII Web site.

• A query can be as simple as words separated by spaces, or it can be constructed using Boolean operators.
• The search engine is not case-sensitive.
• If a word you typed into the search box appears to be misspelled, the NBII search engine will suggest a word from its custom dictionary.
The search begins when you click the Search button, or press the Enter key on your keyboard.

• Geospatial search - click on the Geospatial link above the search box if you want to target your search to a specific geographic area. You will see a Raptor Geospatial search entry screen, which features a four-step process for starting a search:

• Type a keyword or a combination of keywords into a search box.
• Click the "Draw a Bounding Box" button to delineate a region on the map for your search. This step is optional, because if you do not draw a bounding box, the default map extent will be interpreted as a bounding box. Another way to select a region for the search is to zoom on it by means of zooming and panning tools on the map.
• In Geospatial search mode, your search is limited to a subset of Raptor sources which have enough geospatial data in their records to be presented on a map. Step 3 allows you to see the subset of such sources and search against all of them or make your own selections. Click on the  icon to learn more about each of the search sources.
• Start the search by clicking the Search button or reset your search criteria, for example draw a new bounding box, by clicking the Reset button.

• Advanced search – The advanced search interface can be accessed by clicking on "Advanced" above the simple search box at the top right corner of every page of the NBII Web site.

Advanced search helps you to construct a complex query using Boolean and other constraints without having to know the syntax or language of the NBII search engine. The advanced search interface includes the following options (numbers correspond to the screen shot below):

1. Query box: your query is constructed in this box as you fill in the form.
2. Show results with: Use these search boxes to construct your search string and choose where your terms should appear – in the title or anywhere on the page.
3. Sources: Choose which sources to search, or leave the default sources selected. Sources are described more fully below, in the section Advanced Features: Selecting Sources.
4. File format: Select a specific file type to search for.
5. Date range: Select a specific date range for your search,.
6. Number of results for clustering: controls the number of results used for generating clusters. Clusters are explained more in the section Exploring the Results: Clusters.
7. Timeout: adjust the length of time the search engine waits for a source to respond.
8. Results per page: Select the number of results to display on a single page in your browser, showing up to 100 results at a time.

After constructing your search and choosing advanced settings, your search begins when you click the Search button, or press the Enter key on your keyboard.

Boolean Operators

Boolean operators can be used to construct a complex search string containing multiple search terms and conditions. The advanced search allows you to do that without knowing the syntax of the NBII search engine.

OPERATOR	DESCRIPTION
AND	If more than one word was entered in the search box, the NBII search by default returns results that contain all of the search terms. It is not necessary to enter AND between search terms.
OR	Finds documents containing at least one of the specified words of phrases. Duck OR teal finds documents containing either duck or teal. The documents returned may contain both words, but won't necessarily contain both words.
NOT, -	Excludes documents containing the specified word or phrase. flycatcher – willow produces documents with the word flycatcher but not with the word willow.
" "	Finds documents containing the exact phrase in quotations. The search "climate change" would find documents containing this exact phrase rather then any occurrence of the word climate or change.
filetype:type	Finds documents of a particular file type (e.g., .pdf, .xls, .ppt). For example, adding filetype:pdf to your search terms will only produce documents in .pdf format. This feature can be reproduced by using file type refinements on the results page or by constructing your query from the advanced search interface.

Exploring the Results

The results of your search will be listed in order of relevance. In addition to browsing your results one by one, NBII Search provides you with several other powerful ways to navigate your results:

• explore them by clusters - topical categories created on the fly,
• refine your results by predefined navigational categories based on metadata, such as publisher, date, file type, etc. to zero in on what you are searching for,
• visualize your results on a map based on associated geospatial metadata, or
• find images that match your search.

Exploring the Results: Clusters

Clusters are topical categories dynamically generated by the search engine at the time of your search based upon search results.
Use clusters to discover themes contained within documents and to navigate to search results by topic.

• Clicking on the name of a cluster will display the search results contained in that cluster.
• Clicking the plus symbol will expand a cluster, displaying the sub-clusters that it contains.
• The number displayed next to a cluster is the number of unique search results that a cluster contains.
• When a list of clusters is especially long, only the beginning of the list is displayed. To show the next segment of the list, click the "more" link.
• Clicking on remix link will instruct the search engine to re-group the results, revealing different topics in the clusters.
• Clicking on the word Clusters on the top of the tab will take you back to the original set of results after viewing results within a particular cluster.

Exploring the Results: Refinements

 Use refinements when you know what type of document you are looking for. For example, if you are looking for a report that you know is probably published as a PDF file, you can limit your results to display only documents in this format by clicking on PDF in the File Format menu of the refinements box. To deselect a refinement, click on the x next to it in the refine results box or in the refinements bread crumbs line.
Refinement options vary depending on the particular sources being searched - the more metadata the source has, the more refinements can be offered. When searching the default sources, you can refine results by publisher and file type. When viewing image results from the NBII's Library of Images for the Environment (LIFE), date, country, creator, copyrights, and common name can be used for refining the results.

Exploring the Results: Maps

Several map views are used in different ways in the course of your search:

• A map of North America appears in the geospatial search interface; this map can be used for drawing a "bounding box" for designating the geographical limitations of a search. To learn more about starting a search using the map, see the section on Geospatial search.
• After a Geospatial search has been run, an index map appears at the top of the search results list.  The index map indicates the general geographical points of reference to which the items in the results list refer, indicated by pin-drop and other icons. Click the Map legend link at the top of the index map for more information about the map icons.
• Within the results list, an individual map is available for each citation with sufficient geospatial information. Display the map by clicking on the push-pin icon that appears near the title.  This feature works the same way in all Raptor searches.
• Finally, clicking on the pin-drop icon associated with any particular results list citation will cause a "bubble" to appear across the index map.  In that pop-up bubble, for most citations, there will be a button to activate the Data Explorer--a map view in which the data points associated with the search result will be displayed.

Exploring the Results: Images

The first few images resulting from a search of Raptor will be displayed in a preview pane, positioned at the top of the page of results and designated by an Images tab. If there are no images that match your search, no images will appear; try a less restrictive search or a different term.
To access the complete set of image results, select the More images link directly below the preview pane. Images are from the NBII Life and other biological image repositories, and can be refined by different categories than documents or other file types. Available refinements include date, country, creator (photographer), rights (copyright, public domain, etc.), and common name.
To deselect a refinement, click on the cross next to it in the refine results box or in the refinements bread crumbs line.
To return to the main results page, click the link at the top of the page.

Accessing the Results

Click on the title of a search result to open the result page in the full window, replacing the search results page. In addition to the title, each search result includes the source, publisher, and the URL of the search result.

Clicking the Cache link opens the cached version of the page in the full window. Cache is a snapshot of the original page, stored (cached) on a Raptor server. Consider using Cache if the original page is unavailable because of Internet congestion; a down, overloaded, or slow website; or if the page was recently removed from the Web.

If you like a particular result, you might want to try the find similar link next to it. Find similar will start a new search on ten words that the search engine identifies as the most important for the content of that document.
These icons next to the underlined title of the search result give you other viewing options:

• opens the result in a new browser window.
• opens the preview pane, a window which displays the web site without leaving the search results page. The icon will close the preview pane.
• Results with sufficient geospatial information also have the map pin icon , which opens a window, presenting the result on a map.

In Geospatial search mode, results can also be accessed from the information box associated with pin drops on the results map. The information box, or the "bubble" (shown open in the screen shot below), pops up when you click on a pin drop on the results map. It provides basic information about the result – title, publisher, sources, and URL. You can access the result by clicking on the title. The link "Result List" in the bubble will take you to the result citation in the listing below the map, not to the actual result.

Saving the Results

To select individual results you would like to save, use the check box located next to each result in the list. You can also use the select/deselect all on this page check box above the results list to save the results page by page. Tip: you can change the number of results per page up to 100 to increase the amount of results saved at a time.

The option to change the number of results displayed per page can be found at the bottom of the results list, or from the advanced search screen.

You can save the results in a variety of formats, such as text, HTML, XML, or RIS. You can also have your results automatically exported into a citation managers program or an RSS reader of your choice.

Advanced Features

NBII Search provides advanced features, which can help you to adjust your search strategy and increase relevancy of your results.

Advanced Features: Find Similar

For a search user, one of the greatest challenges is selecting the right term to put in the search box. This is what "find similar" can help with. Once a relevant document is found, you can click on the find similar link next to it, and the search solution will retrieve all results that are similar in content to that document, even if they do not include their original query. Find similar will start a new search on ten words that the search engine identifies as the most important for the content of that document.

Advanced Features: Search by Synonyms

Searches are automatically expanded using NBII's Biocomplexity Thesaurus (BCT). This means that when there is a match between a search word and a term in the BCT, the synonym(s) for the search word are automatically added to the search and will be shown above the results list.
If you do not want to take advantage of the expanded search, you will have the option to limit the search to your original search terms.

Advanced Features: Related Topics

If the search word matches a BCT term, related topics will be displayed in the box on the right side above the results list. For example, when you search for "deer" the Related topics box displays the related terms Elk, Game animals, and Ungulates. Clicking on a topic initiates a new search on the term(s).

Advanced Features: Selecting Sources

By default, NBII search covers Web pages and catalogs supported or created by the NBII, as well as related sites on the subject of biodiversity outside of the NBII itself.
Use the Sources tab on the panel to the left of the search results to see all the sources available for search and/or to make your own selections.

• The search sources are organized into three major groupings: NBII, Relates Sites, and Additional Sources. Clicking on the plus symbol will expand a source grouping, displaying the sources that it contains.
• Clicking on the icon will open a box with a brief description of the source or source group.
• Clicking the search button at the end of the sources panel or next to the search box in the banner, will execute your search against the sources you selected. If no selection was made, the search will be conducted in the default sources (NBII and Related Sites).
• Additional sources are not searched by default. Selecting one or several specialized databases from the additional sources group evokes what is known as federated search, or meta search, when the search is conducted remotely and the retrieved results are fetched back to be displayed conveniently in the same NBII interface.

In Geospatial search, the option to select sources is offered to the user when entering search parameters. This was done to let the user know that the Raptor Geospatial search is limited to sources with sufficient geospatial information.

Geospatial Search

Within Geospatial search, we are also working to provide an option to display or preview the geospatially referenced data associated with a result. This option is still in development, and may not be available at all times.

If you click on a pin-drop icon on the index map or next to the title of an item in the results list, the corresponding results citation will appear in a "bubble" over the index map.  Below the citation, if geospatially referenced data is available, you will see a click-able button labeled "View in Data Explorer". Selecting the button will open a specialized map view, with its own display controls, upon which the detailed data will be displayed.

The Data Explorer map is capable of displaying several optional "layers" or map detail overlays that can be made more or less visible according to your preferences. A Google Physical map is used as the base layer; it can be turned off by un-checking the Google Physical box in the Data Panel. The different map layers are listed in the Info Panel to the left of the map. Clicking the "+" sign associated with each map layer type will expand the listing of the color codes, and their meanings, used within each layer. The Info Panel can be hidden by clicking on the arrow; click again to reopen it. "Slider bars" at the base of the Data Explorer map control the opacity of the different layers, and can be used to make any particular layer more or less visible.  A "Print" button in the lower right of the map display lets you print out your customized data map.