Data Entry in Specify :data_entry_:

:specify6: If you are looking for Specify 6 documentation, please see this post.

Data Entry :data_entry_:

Data forms are used for entering, editing and viewing collection data. Because Specify uses related fields to link information, most data can be entered using the Collection Object form, however it may be useful to enter background information, such as Agents and Collecting Events before entering Collection Objects.

Each discipline has access to a specific set of default forms for viewing, entering and editing data.

You can access the data entry dialog by selecting the :data_entry_: Data Entry button in the navigation menu. This dialog will show all of the tables you have configued to display.

You can configure the data entry dialog available tables by selecting the :pencil_: icon to the right of Data Entry.

You can either replicate the Specify 6 settings or customize the tables by selecting Use custom settings and clicking Apply.

You can move tables between the select and possible tables by clicking on the < and > icons between the two columns. You can reorder the select tables by clicking on the and icons on the left.

Unique Data Forms

Working with Forms and Trees

Specify represents Taxon, Geography, Storage, Lithostratigraphy and Chronostratigraphy data in both trees and forms.

When adding, editing or viewing data as a tree, users can also access forms for individual nodes by clicking the Edit button.

Taxon Form

The Taxon form by default includes fields from the Taxon table such as Name, Parent, Rank, Common Name, Source (of the Taxa), Author (this is often the person that described the particular taxa), synonym information, Child Taxa and Taxon Citations.

It also includes information for Hybrids by combining the Hybrid Parent 1 field and the Hybrid Parent 2 field.

Determinations Form

The Determinations form includes many fields that may not be immediately recognizable.

Field Label Field Usage
Preferred Taxon This is a view only field that represents the preferred name of any synonym entered into the Determined Taxon field. If a preferred name is entered into the Determined Taxon Name field then this will represent a duplication of that name.
Current A check box to indicate whether a given determination is current for this specimen. Current Determination is a Required Field but only one can exist for each Collection Object. Therefore; to change the Current Determination one must first open the old Determination and uncheck the Current box.
Taxon This field is the determined name of the specimen in question. Names can be chosen from the existing authority file from a Query Combo Box, or added to the Table. Synonymized names are included in the Query Combo Box, but if chosen a prompt will indicate that the name is a synonym and ask which name to use. This prompt can be turned on by choosing Specify > Preferences > Trees on a Macintosh or Edit > Preferences >Trees on Windows or Linux and checking the Prompt to Replace Taxon with Preferred Taxon box. This field operates as an “either/or” condition with Alternate Name; both cannot be entered in a single Determination.
Qualifier A term to qualify the identification of the taxon name when doubts have arisen as to its identity or as a comparison to a given name (e.g. “cf.” or “aff.”).
Addendum A Pick List suffix element added to the taxon name to indicate a concept or citation for that name. For example; sensu lato.
Type Status Name A pick list of all available type designations; Holotype, Paratype, Neotype. Specify ships with predetermined values which are editable for users.

Botany and Entomology Taxon forms will also have these two fields:

Alternate Name A free text field for insertion of a name (scientific or common) not recognized in the taxon tree authority. This field operates as an “either/or” condition with Preferred Taxon; both cannot be entered in a single Determination.
Name Usage User customizable pick list used to describe the context of the name entered into the taxon or Alternate name fields. Taxon field - if a synonym name is used, it could denote a “shelved by” name. Alternate name field - could denote the appropriate authority the alternate name was taken from (e.g. Flora of Nebraska).

Alternate Name

A free text field for insertion of a name (scientific or common) not recognized in the taxon tree authority. This field operates as an “either/or” condition with Preferred Taxon; both cannot be entered in a single Determination.

Name Usage

User customizable pick list used to describe the context of the name entered into the taxon or Alternate name fields. Taxon field - if a synonym name is used, it could denote a “shelved by” name. Alternate name field - could denote the appropriate authority the alternate name was taken from (e.g. Flora of Nebraska).

Locality Form

The Locality form allows the user to enter the latitude and longitude information within the Coordinates section of the form.

The only characters that are allowed in the input field for coordinate fields are:

  • A whitespace character (tab, space)
  • A digit
  • Any of the following: "'-.:ensw° (case-insensitive)

When a lat/long is entered the format is captured and displayed in the (Source) field. This field remains constant when formats are changed, but if the lat/long numbers are changed then the (Source) field will update to the new lat/long entry.

Note: Specify does not track versions of the latitude and longitude and does not keep a verbatim field. You can add verbatimLongitude and verbatimLongitude to the form if you would like to store this information!

Latitude1 and Longitude1 are Decimal fields, automatically filled in after data is entered into the form or uploaded through the WorkBench. The data presented on the form and entered into the database are stored in the Lat1Text and Long1Text as a String.

Other data on the Locality form include a Geo Referencing Determination By and Date. These are for documenting how and when a georeference for the Locality occurred.

Locality Plugins

GEOLocate

The GEOLocate project has created software and services for translating textual locality descriptions associated with biodiversity collections data into geographic coordinates. It uses a description of a Locality and geography fields, such as County, State and Country, to find Latitude and Longitude coordinate values. This is referred to as georeferencing. The Specify and GEOLocate teams have collaborated to create a GEOLocate module inside Specify.

For Georeferencing United States localities:

Column Data Needed
Locality Name Yes
Country Yes
State Yes
County No, but will improve results(Required when searching waterbody and highway crossings)
Latitude1 No (this is the results column)
Longitude1 No (this is the results column)

For Georeferencing localities outside of the United States:

Column Data Needed
Locality Name Yes
Country Yes
Child Node of Country No, but will improve results
Latitude1 No (this is the results column)
Longitude1 No (this is the results column)

GEOLocate will show you any possible locations it can find based on the information in your columns. You can zoom, scroll, and navigate the GEOLocate web application within Specify. You can edit the uncertainty, add pins, and draw polygons.

You can view and modify the locality, country, state, and county from the GEOLocate window. Click Georeference to search the modified query.

Boolean fields in GEOLocate

Placing a marker will change your point’s latitude and longitude and move the uncertainty radius around with it.

The green selected marker is the value for the most accurate result. This will be saved when you save this to your application.

Measuring allows you to click anywhere on the map, move your mouse to measure a distance, and double click to finish the measurement. It will display in kilometers and miles.

This text box shows the Lat1, Long1, Uncertainty radius in meters, and the coordinates of your polygon’s points.

Draw a polygon by clicking on map for each point in your polygon. Once you are finished creating it, double click the mouse. You can clear your polygon to draw a new one.

You can save the information created on GEOLocate to Specify if you have the correct columns in your Data Set. The information will be fed directly to the WorkBench once you click the button at the bottom of the window.

Under the Workbench tab in GEOLocate’s interface, you can click to configure the georeferencing options.

• Match Water Body - When enabled, GEOLocate will search the locality string for bridge crossing information and attempt to pinpoint the locality at the intersection of the river and highway. This feature only works for U.S. localities and requires county data.

Detect Hwy/River Crossing - When enabled, GEOLocate will search the locality string for the names of rivers and streams. If one is found, GEOLocate will snap the calculated points to the nearest point on the waterbody. This feature only works for U.S. localities and requires county data.

Do Uncertainty - When enabled GEOLocate will calculate and return the uncertainty radius if one exists.

Do Error Polygon - When enabled GEOLocate will calculate and return the error polygon.

Displace Polygon - When enabled GEOLocate will use any distance value referred to in the Locality Description to displace the GEOLocate Error Polygon value (if one exists). If 10 miles North of Lawrence is in the Locality Description, but the Error Polygon in GEOLocate is a 30-mile radius around the center of Lawrence, GEOLocate will move the 30-mile radius 10 miles North of the center of Lawrence.

Restrict to Lowest Adm. Unit - When enabled limits results found by GEOLocate to points within the lowest administrative unit in the locality description.

Language - Tells GEOLocate what language to use for the Locality interpretation.

GEOLocate Definitions

  • Position represents the Latitude and Longitude of the GEOLocate result, visually depicted on the map as a green marker. These results can be edited.
  • Markers represents the Latitude and Longitude of a GEOLocate point, visually depicted on the map as a red marker. These will be become a green marker if it is the selected position.
  • Uncertainty Radius represents the error due to the uncertainty of the locality information provided. It is shown as a grey circle around the green point marker on the map. The Uncertainty Radius can also be edited.
  • Latitude represents the latitude to the hundredth degree.
  • Longitude represents the longitude to the hundredth degree.
  • Pattern, or pattern identifier, is a text description of the pattern or keyword used to determine a GEOLocate result. Single locality strings often include multiple patterns, producing multiple GEOLocate results.
  • Precision is an indication of the quality of locality information. Each GEOLocate result is given a score between 0 and 100 which represents the probability of it being a match. That score is then placed within a ‘low’, ‘medium’ and ‘high’ ranking to indicate precision. Results are then ordered according to their probability number, which allows results within the same rank to include the most accurate matches first.
  • Error Polygon is a polygon which encompasses the entire area of uncertainty.
  • Uncertainty represents the error due to the uncertainty of the locality information provided.

Specify uses the embedded client from GEOLocate. For more documentation, visit their website https://www.geo-locate.org/.
All Specify interactions are managed by the Specify Software.

GeoMap

GeoMap plots all the points in your selection on the map. It uses OpenStreetMap, ESRI, Géoportail, USGS, and NASA maps to give a multitude of viewing options.

Icon Use
Toggle the full screen view
Zoom in and out on the map
Change the map type as well as enable or disable labels, boundaries, pins, polygons, polygon boundaries, and error radiuses
Click to view all details about the pin
When full screen view is enabled, this allows the user to print the current map view, including pin details if activated

Collecting Event / Time and Place

One of the important curatorial decisions to be made early on is the use of “Collecting Events” in a collection. This is also named ‘Time and Place’ on some Data Type forms. A collecting event is described by the date and time of the collection together with collector names and a number associated either with all specimens collected at that date and time or a number associated with each individual specimen.

In the first case (traditionally used in lot based collections) the number is associated with the Collecting Event itself (and all its associated data) in the form of a Station or Field Number and is therefore associated with one or many specimens or collection objects collected at the same time and place by the same collectors e.g. ACB 09-01. The Station or Field number thus describes all specimens or Collection Objects collected at that time and place. There is a many-to-one relationship between specimens, or Collection Object and “Collecting Events”. In this instance, the Collecting Event form is usually expressed as a Query Combo Box on the Collection Object form so that values can be searched, and the same collecting event can be used (based on the Station/Field Number) for entering information for multiple specimens without having to enter it repeatedly. The data displayed within the Query Combo Box is then formatted using the schema definition to display a textual string representing the different data elements of the Collecting Event (Field Number, Date, Geography and Locality information). The lookup function of the Query Combo Box will also display this format to aid in selecting the correct Collecting Event for subsequent specimens.

In the alternate case (used by all other disciplines) the number is associated with each individual specimen or Collection Object in the form of a Collector number - a unique number given to every specimen collected and usually including the Collectors acronym e.g. ACB 12345, while the remaining data is still bound to the Collecting Event table. There is a one-to-one relationship between specimens and Collecting Events. In this instance the Collector number would be a field on the Collection Object form and all other fields would be associated with the Collecting Event which would not include a Station/Field Number and would be expressed as an embedded sub form on the Collection Object form and would not be able to be reused for subsequent specimens.

Disciplines traditionally use one of these two methods.

A method should be chosen before data is entered, uploaded, or migrated into your database by our staff. To facilitate our set up of forms for evaluation, we have set defaults for collection types and Specify ships with all Disciplines except Ichthyology using Collection Event as a one-to-one relationship.

If the default form does not represent the way you process collections, and you are unable to change the setting after following the instructions, you can create a new post in the #members category or contact us at support@specifysoftware.org.

Specify 6 Configuration:

If forms are changed from a one-to-one relationship to a one-to-many relationship the checkbox for ‘Add Collecting Event Automatically’ on the Collection form (System > System Setup > Configuration) will need to be unchecked after importing the new form.

Agent Form

An Agent is not limited to single individuals. The Agent Type field on the Agent form allows an agent to be the following:

Agent Type Usage
Person This is an individual with field options of first, middle and last name, abbreviation, email and multiple addresses and attachments.
Organization This is often an Institution with name, abbreviation, email and multiple addresses and attachments.
Group Using a group option allows multiple agents to be associated with one name entity. This type of Agent includes name, abbreviation, email and links to individual Agents that are a part of the group. This option is useful when it is necessary to search by the group name.
Other Other is used when the other three options do not apply. Name and attachments are the only fields for this agent type.

It is also important to note that Agents are shared throughout a Division. In other words, if a division has two disciplines (A and B) and division A creates an Agent, division B, as well as all collections within the two divisions, will also have access to that agent.

Preparation Form

It is important to note that the Is On Loan checkbox is for display purposes only. This information is updated when a loan is created or edited. The Preparation Type field is a Pick List.

Attachments Form

Many tables in Specify allow Attachments. When a file is attached, Specify creates an attachment record in the database with the original name, mime-type and most importantly, the path to the file in the repository, or attachment location. Attachments are not stored in the database. Specify makes a copy of the attachment, renames it with a unique name, and stores it in the attachment location specified at the database level.

The Specify Wizard creates a default path and location for the copied attachments, but it is recommended that the user create a unique location by editing the default path within the System Preferences. The attachment storage can either be located on a local drive, a server or an attachment server. To create and/or alter the attachment location, go to:

Note: Thumbnails are also created for jpg, png and most pdfs, which can be viewed on the attachment form. Other file types are represented by a default thumbnail based on their file type.

If a path does not exist or Specify is not able to connect to the path, the attachment will not be saved and an error will be thrown.

Note: Specify can accept images in a tiff format, but they can not be displayed in Specify, a default thumbnail will display on the form.

Attach Files

Attachments button

When presented in this view, files can be directly dragged on the box or it can be clicked on and you can pick a file from your file manager.

You can attach files to any supported table (see all tables with an “{tablename}Attachments” field) record with an attachment button or subview.

Paleo Context

Paleo data table relationships can link specimens to PaleoContext via the relationship which best fits their conceptualization and linking preferences. Specify has the default relationship of Paleo Context linked to the Collecting Event table as a 1-to-Many relationship, but this relationship can be altered to a 1-to-1 relationship through manipulation of the form structure. Paleo Context can, in much the same way, can also be linked to the Collection Object and Locality tables with either a 1-to-Many or 1-to-1 relationship using a similar form and database schema modification. The Paleo Context relationship is required to be the same for each collection that resides in the same Discipline and database.

Collections using a 1-to-1 relationship require Paleo Context information to be entered for each specimen and do not allow for the data to be used by other collection objects.

Embedded paleo forms will be displayed as a subview.

In the case of 1-to-Many relationships, the customized forms will include a drop-down query-combo box for searching for and/or selecting from existing Paleo Context records, which can then be shared within collections residing in the same Discipline within the same database. Adding, editing and viewing the Paleo Context is accomplished through the query-combo box tools which will open a new Paleo Context form window.

Non-embedded paleo forms will display as a Query Combo Box.

For more information regarding Paleo Context and customizing forms members of the Specify Collections Consortium may contact the Specify team at support@specifysoftware.org.

GUID

GUIDs in Specify are generated using a 128-bit Universally Unique Identifier, or UUID (example: bf3066d2-c088-47c8-b279-e7941463a65f0). Newly created collection data records will be assigned UUID values in all tables with GUID fields (except for Geography and Taxon) when they are created.

Specify automatically creates GUIDs in the GUID field of the following tables:

  • Agent
  • Attachment
  • Collection
  • Collecting Event
  • Collection Object
  • Determination
  • Geologic Time Period
  • Institution
  • Journal
  • Litho Stratigraphy
  • Locality
  • Reference Work

Note: GUID’s are unique for each database instance; institutions storing their collection data in more than one database will also acquire unique GUID’s for each database.

Using a GUID to identify information allows it to be shared and recognized as being unique

Specify Network :spnetwork:

The Specify Collections Consortium has partnered with the Lifemapper project and the larger community to link services that increase the exposure, utility, and curation of collections worldwide. For instance, if your information is sent to GBIF then opening a collection object record in your collection and clicking the Specify Network button will send the specimen ID information for the specimen to the Specify Network service and a summary page will be presented, showing published information and data cleanup metrics from GBIF. Similarly, it will display species distribution information from Lifemapper using all occurrence points for that species in GBIF. We are constantly looking for new sources of shared information, if you know of a resource that is not shown on the web page for your specimen please let us know. We are also updating the Specify Network to create colection-level analytics assessing the composition of collection holdings and available species information. These data are used to compare and assess collections against and among the collective holdings of all published collections. This information is then made available back to the institutions and the community so that it can assist those collections in prioritizing collecting and digitization efforts