Conducting a Search

The key to getting the most out of Arctos is learning to search effectively. More often than not, a task will specify a specimen by MVZ number, or a group of specimens by their Accession. In these cases, your search will consist of only one step. Occasionally, however, you will be asked to find a list of specimens without using these numbers. Fortunately, Arctos’ powerful search feature will help you get there.

The homepage of Arctos is also its search feature. That is your signal that you will be seeing this page a lot, so you will very quickly grow familiar with it. This guide explains some of the most commonly used search features.

You do not need to create an account or login to search. However, there are some features (e.g., downloading records) that require you to login.

Identifiers

Any ID

Identification and Taxonomy

Locality

Spatial

Spatial Search provides spatial tools which consider both asserted and derived data. A (very) brief overview of Arctos is necessary to understand how these tools function.

Any Geographic Element considers asserted locality and geography terms, plus geography search terms, plus terms pulled from various spatial query services including Arctos, GBIF, and GeoLocate. This field is intended to cast the broadest possible net, and should be expected to find unintended records (or false positives).

Map Polygon - zoom and pan the map to the area of interest, click the polygon icon (top-center, next to the ‘stop drawing’ hand), then click the vertices to create a polygon. (Doubleclick or click the hand to close the polygon; the search will fail without this critical step.)

Geography Shape Name searches by geographic shapes, regardless of assertions. That is, a search for A will find records where the locality “insersects” (see Spatial Match Type) the named geography, even if the geographic assertion is for Z.

Spatial Match Type is coupled with polygon tools (Map Polygon, Geography Shape Name, KML). 4 options are available

Place Term Type together with Place Term are essentially Any Geographic Element with more control; these are terms gathered from various sources, but here it is possible to type them (for example, ‘term as understood by GADM2’)

Locality Attributes Magic

Age and Chronostratigraphy are ‘metadata terms’ from various sources which provide less-specific ways to find localities. For example, a metadata query for Cisuralian will find assertions for Asselian because of a Cisuralian includes Asselian assertion in the ctchronostrat_series_epoch code table metadata.

The Rest

The rest of the locality section is limited to direct assertions. A search for Locality Attribute Value “Jurassic” will find “Jurassic” and nothing else (and assertions are generally to lithostratigraphic elements or finer-scales chronostratigraphic elements). A search for county=X will find records with that assertion and nothing else; it will find records that have the assertion but map elsewhere, and will not find records which map to the county but have a state-level assertion.

Examples

Example: Named Shape Contains

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Finds all records from a named shape, even when the assertion does not include that shape. Records for which county-level geography is not specified are included when the locality assertion is entirely contained within the county.

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Example: Named Shape Intersects

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Finds all records which intersect (“might be from”) the named shape. The following record is found, despite claiming to be from a specific county in another state, because the asserted error intersects (encompasses in this case) the specified shape.

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Example: Named Shape Does Not Contain

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Finds the same record as above - one which claims to be from a specific county, but has error which extends beyond that county. This kind of search can be useful in finding problematic records in need of more attention, or understanding to what extent asserted data might be trusted for some particular operation.

This query can also be performed from /place.cfm. Searching for geography, or clicking the link from one of the misplaced records located in the above search menus, provides a shortcut menu:

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Example: Drawn Shape Contains

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Works precisely the same as ‘Named Shape Contains’, but uses an arbitrarily drawn shape rather than the shape associated with a geography record in Arctos. This approach can be useful when Arctos does not contain an appropriate geographic element - a three-county area, for example.

Example: KML Shape Contains

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Works like other polygon queries, but from KML. For example, this can provide a repeatable way to query for a three-county area. Note that the KML understood (via PostGIS’ ST_GeomFromKML()) is very limited.

That’s nice, but I need to….

File an Issue! Spatial capabilities are relatively new to Arctos, we know we haven’t explored all possibilities, and as a Community-driven resource we are always excited to hear ideas for improvement. We will adjust the User Interface to accommodate your needs if we can, and we can usually provide data if we can’t (or can’t immediately).

Date/Collector

Biological Individual

Relationships

Relationship

Relationship is applied to found specimens. “Eaten by” will find kangaroo rats eaten by snakes; “ate” will find the snake which consumed the rat.

Related Identifier Type is the type of ID establishing the relationship, and is drawn from CTCOLL_OTHER_ID_TYPE

Term and Value

Term and Value are key-value pairs drawn from the related specimen’s data.

Usage

Media

Customizing Results of a Search

The default Specimens Result page provides a pretty comprehensive overview of each specimen and its relevant locality information. The most important fields you will pay the most attention to are GUID, Identification, Specific Locality, Dec. Lat., Dec. Long., and Max Error. Even though these are already present on the page, different tasks may require you to modify your results out of convenience or necessity.

Specimen Search Refine Widget

Click [ Show/Hide Search Terms ] to add or remove an inline search form.

Search Terms Widget screenshot

This tool is extremely network-intensive; use with caution.

The tool uses intensive caching, and changes to documentation or data may not appear for about an hour.

The form consists to 4 columns:

Terms which were included in your current search Select terms from your search results, based on your preferences (from “add/remove search terms”) The option to add any available search term Mouse-over terms for minimal documentation, click for full documentation, links to controlled vocabularies and definitions, etc.

Value is term-specific. Some terms will only accept case-sensitive exact matches, some will accept substrings, and some will accept operators (such as “=” prefix to indicate exact match only). Most term will accept value “_” (underbar) to mean “match anything” or “require this attribute.” (Note that Arctos is highly normalized, and most terms do not exist for most specimens, while some specimens may have multiple values of any term, such as multiple numeric age determinations based on the cementum layers of different teeth.)

Vocabulary includes suggestions from code tables , unique values from some tables (such as Geog_Auth_Rec.Country), and operators from documentation. Data in this column are suggestions only; selecting them will simple push a value to the Value column, which you may then remove, alter, or re-query. Values in the Vocabulary columns are themselves ignored. The Vocabulary column may be incomplete, unused in the current dataset, incompatible with other parameters (e.g., State=Alaska + Country=Somalia should not find anything), or otherwise irrelevant or confusing.

One or two options (depending on current search terms, vocabulary controls, and what’s turned on in your results set) may be available when vocabulary suggestions are available. (Some terms will not provide suggestions due to indirect mapping between the highly-structured database and the “flattened” query view.)

Fetch all will return all available terms, with terms included in results in bold. For example, if you’ve searched for Sorex palustris and United States, fetch all in State will return a few hundred states, and Alaska, California, etc., will be in bold. Selecting any bold value and re-querying will return a subset of the data. Selecting “Yukon Territory” will return nothing, but selecting Yukon Territory and removing United States will produce results. Use this for exploration. Fetch from results will return only those values which exist in your search results. Selecting any value from this list (they will all be bold) will return a subset of the search results; this is a way of drilling down from a general search to more specific records. Blank Value does not include the term in subsequent searches. _ (underbar) requires the term to exist, but does not filter by value. Underbar will not work for some terms; we’re working on documentation.

Maps

If you query by coordinates (“Select on Google Map” search), the map will zoom to contain APPROXIMATELY the area you queried. (Exact fit is not implemented due to limitations of the Google Maps API.)

Under the map, click “QueryByViewport” to add the coordinates of the visible map to your search. Note that the results will, as above, zoom to only approximately the area you selected.

Warnings

This form is in beta development. Some term/value pairs are dependent, and some will be somewhat nonsensical in this format. Please use the Contact link at the bottom of the page if you find something cryptic, nonfunctional, or just have a great idea for improvement.

Saving Searches

Occasionally, you will be assigned a task that you may not be able to complete in one session. If the search parameters are simple, it would be easy to execute the search the next time and resume working. If you have modified the results or wish to share your search with someone, it would be helpful to save your search.