Specify 5 FAQ
- Releases and Support
- Hardware and Software
- Usability and Configuration
- Catalog Numbers
- Data Retrieval
- Importing and Exporting Data
- Web Access
- Authority Files
- Loans, Accessions and Permits
What is the Specify Software Project?
The Specify Software Project is a biological collections informatics initiative. Its mission is to facilitate effective utilization of biological specimen data for scientific research and applied uses, by supporting zoological museums and herbaria with collections management software, data management, help desk services, and training.
The Specify Software Lab is a part of the Informatics Department of the Biodiversity Research Center at the University of Kansas. Project staff include a director, manager, professional software developers, helpdesk support manager, data management specialist and software quality testers. Specify is available at no charge from http://www.specifysoftware.org, and it is supported for non-profit, biological collection institutions. With its predecessor, the MUSE Project, the Specify Software Project has received 20 years of funding from the U.S. National Science Foundation.
What does Specify do?
Specify is a Microsoft Windows database application for the entry, management and retrieval of data associated with biological collections. This information includes specimen locality descriptions, geospatial coordinates, taxonomic determinations, collector and date information, specimen properties such as morphology, preparation type, as well as ecological features associated with collection localities. Specify is also designed to support collection curation; it manages data for loans, accessions, deaccessions, exchanges and other transactions. The program includes an integrated, flexible, report designer for customizing printed labels and reports. Specify also has full-featured web server interfaces for publishing collection data as HTML pages, and in XML for provision of structured records to disciplinary networks and to the Global Biodiversity Information Facility, GBIF.
Which operating systems does Specify run on? Does it support multi-user access?
Our latest release, Specify 5.2.3, is supported on Microsoft Windows 2000, 2003 Server, XP Pro and Vista Business PCs. A Specify database can be installed on a modest workstation or on a larger dedicated server for simultaneous network access from multiple local machines. Specify 5.2.3 can use Microsoft SQL Server 2000 or SQL Server Desktop Engine 2000 (MSDE) as its data manager, but SQL Server 2005 Express Edition or another SQL Server 2005 edition are preferred.
Which disciplines does the program support?
Taxonomic disciplines supported by Specify are: mammalogy, ornithology, ichthyology, paleontology, invertebrates, botany, herpetology, and entomology. Mineralogy, ethnology, anthropology and living collections are not supported, because our data model and software functions are not designed to meet the needs of those fields.
Can I manage all of my institution's biological collections data with Specify?
Specify can easily manage specimen data from multiple taxonomic disciplines. There are two site configuration scenarios. (1) You may choose to create separate Specify installations to operate as distinct databases for different kinds of collections. This is usually the preferred configuration at institutions where collections are administrated and managed in different divisions or departments. (2) Alternatively, by defining two or more taxonomic types within a single Specify database, an institution can combine data across disciplines and support cross-disciplinary data entry, retrieval and reporting. This second approach simplifies database administration, as only a single database and database server machine is needed. Some data entry/edit forms in this scenario are duplicated to allow customization by discipline, some data forms are shared across disciplines.
Within a defined taxonomic collection type, Specify supports one or more collection series. Collection series are a way to subset a given taxonomic collection when it is necessary to identify members of two or more administratively or legally distinct collections. For example, a set of plant specimens in a teaching collection can be distinguished from the primary herbarium collection, though both would be cataloged together and fully searchable as a single dartabase.
Specify also supports the practice of having multiple preparation types for any given taxonomic collection type. For example in botany, preparation types might include: herbarium specimens, pollen microscope slides, seeds, dried fruits, photographs, tissues, or extracted DNA aliquots.
Why the name "Specify"?
"Specify" is intended to evoke a sense of "species" and of the systematist's role in specifying identifications.
Will you continue to produce upgrades to the program at no cost?
We have no plans to charge for Specify software.
Is the Specify data model available?
Specify's data model is large with over 70 science data tables and it is downloadable from the Specify Software Project web site. A simplified conceptual data model is also available on the web site. One can access the SQL Server/MSDE schema directly with client database design tools (such as SQL Server Enterprise Manager, or SQL Server Management Studio Express). The Specify data model was derived from the output of U.S. NSF-funded national workshops in the 1990s, led by Dr. Julian Humphries. Dr. Stan Blum completed the model under the aegis of the Natural Science Collections Alliance Committee on Collections and Networking. A primary objective of those meetings was to abstract collections data concepts to a high level, so that data from all taxonomic disciplines could be integrated into a single database, and supported with a single body of software code. We implemented that model in Specify and have extended it since to accommodate evolving requirements.
How many fields are in the database?
There are around 800 fields and 70 data tables in Specify. Specify stores its data form definitions and site customization parameters in additional system database tables which are invisible to the user.
Which programming language is Specify written in?
Specify 5.2.3 is coded in Delphi 2006, an object-oriented Pascal language from Borland (www.borland.com). Data are managed in Microsoft SQL Server or in Microsoft Desktop Engine. The integrated report writer in Specify is based on "Rave 6" from Nevrona Designs (www.nevrona.com). The next major release of Specify, version 6, due out in early 2008, is coded in Java in a cross-platform, extensible, component architecture.
Can I have the source code to modify?
Specify source code is available upon request under the General Public License. We cannot provide the source for libraries we license for the Rave reporting system.
When will the program be available?
Our latest release Specify 5.2.3, is available from: http://www.specifysoftware.org. We issue about one major release per year and maintenance releases as needed. Specify 6, scheduled for release in early 2008 is an entirely new product. Specify 6 is an application platform designed for evolving the database schema, business logic, user interface and web services.
How is Specify licensed?
Anyone can download Specify and use it. The Specify Project will provide installation, training, customization, helpdesk and strategic planning support to research biological repositories that use Specify as their primary, production, collections management system. It is licensed under the terms of the GPL.
Support priority is offered to registered U.S. institutions, but we provide support to non-US institutions as resources allow.
Can I run Specify on my MacBook, Linux box, Beowulf Cluster, Blue Horizon or on my iPhone?
Not yet. Specify 5.x runs under Parallels on an Intel Mac laptop, but that's cheating. Specify 6, scheduled for release in early 2008, is written in Java and will run cross platform on Windows, Mac OS X and Linux. The first component of Specify 6, the Specify WorkBench, is available now for the three operating systems from the Specify 6 web site. Specify 6 WorkBench operates with the Derby (JavaDB) data manager and can be run completely from a USB memory key for the utmost in portability.
Do I need Microsoft SQL Server to use Specify?
Yes, the current release works with MS SQL Server in one of these four versions: SQL Server 2000, SQL Server Desktop Engine 2000 (MSDE), SQL Server 2005 or SQL Server 2005 Express Edition.
How much disk space does Specify require?
Specify and its database manager require about 100 MB with the sample "Demofish" and blank databases we provide, and more space if you have your own data already computerized.
What PC hardware do I need to run the software?
Specify runs best on a PC with 2 GB of memory and processor speeds of 3 Ghz or greater. A standard disk drive of 20 GB or larger is sufficient for most collections. We strongly recommend a CD-RW drive, DVD burner or a tape device for daily backups, if your database is not backed up by your network administrator. We also minimally recommend a SVGA video display monitor (1024x768).
Can I run Specify for multiple user access on my local network?
Sure, one can install Specify on a Windows workstation with SQL Server 2005 Express Edition and configure it for multiple user access. SQL Server 2005 Express Edition (like MSDE before it) has built-in limitations for more than about five simultaneous users. If you expect to have more than 3-4 or more users frequently run Specify simultaneously on your network, it would be better to purchase an MS SQL Server 2005 license and configure a dedicated server machine. Workstations with Specify installed would then access data in SQL Server 2005 on that machine over your local, building or campus LAN. For adequate performance, server and workstations should be connected with a 100 Mb Ethernet network when configuring Specify in a multiple user, client/server setup.
How many records can I enter in an hour?
This is highly variable and will largely depend on the number of data fields you need to complete and the extent to which you have streamlined the data entry process. We work with collections to optimize Specify's data forms. Specify supports "Series Processing" of record batches which greatly speeds data entry for disciplines where taxon and locality data are common for a sequential group of specimens. Also, Specify 5.2.3 has the capability to create an endless number of customized forms, in "Form Sets" so that data entry procedures can be optimized for specific project functions or for particular kinds of users.
Can I change the field captions and data entry field order?
Yes, you can change all the field captions and form titles to something more intuitive for you. All data entry fields can be moved within forms to change the order of data entry. The level of customization possible with Specify data entry forms is quite extraordinary. Fields can be added, removed, moved to a different location or re-named. Customized help information or "usage notes" for each field can be popped up with a right click in mouse-overs when the cursor is located over a field name.
Can I change the type size of the program display?
The type size is dependent upon the font size settings in the Windows "Control Panel/Display" option. The size of your monitor will change the "look-and-feel" of the program; we recommend 17" or larger. We plan to increase the flexibility for configuring font sizes in future releases.
Can I add new fields if I do not find the ones I need in your program?
Yes, tables have auxiliary fields for text, numbers, data, and yes/no type fields. They are found in the accession, collection object, loan, agent and locality tables, among others.
How can I ensure that the data in my database is entered correctly?
You can use the format templates (i.e. "masks") given for data fields, the ranges and number of decimal places for number fields, and the pick lists for exact data entry in list box fields.
Can I enter a specimen when I do not know the determination?
Yes, you can enter a record for an unidentified specimen and add a determination later. You need to identify the specimen as a member of a taxon at some level--to a family, order, subclass or at least to kingdom. If you don't know what kingdom it is, don't call us.
Can I keep track of the history of determinations of a specimen?
Yes, Specify retains all of the information associated with previous taxonomic determinations of a specimen. One determination is flagged as current. Searching and retrieval can be limited to just current identifications, or you can query for any specimen that had ever used a certain name, even if, subsequently, it had been re-identified as something else.
What if I have observations and no specimens?
You can catalog an observation without having an actual specimen, although we give that observation a catalog number for a unique identifier.
Can I use a European date format?
Yes, there are six types of dates in the program including European date format. They are:
YYYY/MM/DD 1996/05/23 MM/DD/YY 05/23/96 MM/DD/YYYY 05/23/1996 DD/MM/YY 23/05/96 DD/MM/YYYY 23/05/1996 DD/MMM/YY 23/May/96 DD/MMM/YYYY 23/May/1996
Can I enter partial dates?
Dates with accuracy only to the year or month can be entered. For example, using the "YYYY/MM/DD" mask, the entries "1950/__/__" and "1950/05/__" would represent "sometime in 1950" and "May of 1950."
Can I enter township/section/range, or latitude/longitude, or UTM or grid mapping (European) coordinates in the program?
The program will store all latitude/longitude data as decimal, however you may enter the data in other formats. Other types of location data such as township, range, section may be entered. We've added new capabilities for handling latitude and longitude values to accurately record the precision and format of the original data entry and to accommodate new georeferencing standards, such as those of the Mammals Networked Information Service (MaNIS).
Do you have files containing geographic data, for example city, county, state, country, so that I do not have to enter all the information if I know the city?
We include a data table with Specify which contains the Getty Thesaurus of Geographic Names. This will allow you to import verified, authenticated names into your locality records. In addition, you will be able to check for accuracy of data (for example, Kansas must be in USA ... although Dorothy, Glinda and Mombi may be elsewhere).
Can I track the previous catalog number of a specimen from a previous ledger or system?
Yes, Specify can keep track of any number of previous catalog numbers or other identifiers for a collection object.
What combination of letters and numbers can I have in a catalog number series?
There are several elements to a number series:
Component Field Type Allowable entry Institution identification Text (without mask) Text (without mask) Collection name Text Text (without mask) Catalog Number NumberMask 0-9, with a mask for adding periods and other separators. Sub Number Text Text or Number (without mask) Name Text Text or Number (without mask) Modifier Text Text or Number (without mask
Examples of allowable catalog number series:
KU MAIN 12345.12
MVZ 1998.123-wing, left
UT TEACH 1234.1998.009ABC, skull
I have a rock slab with more than one type of specimen on it; can I give them different catalog numbers even though they are contained together?
Yes, you can give each specimen on a single substrate a different specimen catalog number.
I have jars with numerous specimens. Can I catalog more than one specimen with the same catalog number?
Yes, you may keep a 'lot' of specimens with the same catalog number, or you may have one container with multiple specimens all from the same location with different catalog numbers.
Can I catalog multiple preparations with the same catalog number?
Yes. For example, a skin, skeleton and tissue sample may all have the same catalog number.
Can I search on any data field?
Yes, you can query on any single field or on any combination of fields in Specify. Specify's flexibility for constructing simple or complex, field-based queries is extraordinary. Additionally, Specify 5 introduced full-text, Google-like searching, for extremely rapid retrieval of text from anywhere in the database as a streamlined alternative to conventional, structured field searches. Specify administrators set up search indexes in advance as part of the installation of Specify for all fields that should be full-text searchable.
Do I need additional software to retrieve or export data, or to create printed reports of Specify data?
For the time being, if you plan to export collection data from MSDE or from SQL Server, from within the Window's interface, and you do not already have Microsoft Access installed on your computer, you will need to download and install the MS Access 2000 Runtime Installation Package. This can downloaded from our Specify Software Project download page. Specify's web and DiGIR interfaces are alternative paths for sharing and exporting structured specimen data from your database with others.
Can I save frequently used queries and re-use them?
Yes, conventional field-structured queries can be saved for re-use. Specific search parameter values are then specified each time the query is run. In that way, one can store frequently-used queries and modify the search details as needed. Likewise, printed reports can be created and saved for running at a later time. Specify 5 also allows users to save commonly used field-structured queries as links on the left pane Navigation Panel.
Can I search on text stored within free text remarks fields?
Sure, there are two ways to do this. One can search "remarks" or "notes" fields with conventional field-structured searches utilizing the "contains" operator, or if the Specify Administrator has indexed the table and fields containing the information of interest, then the Express Search option would be an easy way to do this.
Does Specify create distribution maps?
Specify does not produce distribution maps, but we are exploring the use of external web mapping services to generate maps of specimen localities within a Specify program window.
Can I import the data from my Paradox, Dbase, FoxPro, MUSE, etc., database into Specify?
Due to Specify's complex and highly-normalized data model, a programmer's knowledge of data tables and collection data semantics is required to import data into Specify. The Specify Project will transform and copy existing databases into the Specify format for institutional users that are ready to use Specify and have registered. If you are interested in data conversion to use with Specify, please let us know. The Specify 6 WorkBench is designed to map data into Specify 6's schema and Workbench data will be uploadable into Specify 6 by users.
Does Specify manage image and sound data?
Specify allows you to keep attribute data about images and sound recordings such as the number, type, content, date, collector/photographer, etc. in appropriate data fields and also allows Internet and file system URLs to be stored in fields. When clicked, Specify opens the default windows player application for that file type, typically an image viewer, web browser or audio player. In that way, one can maintain links to associated binary data files, such as images, and access them through records in Specify. The demonstration Specify database shipped in the Specify 5.2.3 installation package, "Fishdemo" has several examples of image files linked to collection object (specimen) records.
Can I export data to create mailing or other labels in Word or another word processor?
You can customize, create, sort and print any number of designs of reports and labels directly from the report system without using another program. You can also export the results from any query into a delimited text file or to an external data table.
Can I enter data into more than one database and merge them later? For example, one database is on the laptop I take into the field and I want to merge it with the database on a desk computer in my office.
Specify 5 does not support merging of separate Specify databases.
Can I import my own taxon dictionary into the database?
Yes. Specify has an import function for taxonomic data that are formatted in the Integrated Taxonomic Information System's Taxonomic Workbench database schema (tables). Specify stores names and classification relationships in a taxonomic dictionary which can be used as an index and source of available names for your collection. You can add new taxonomic names and classification relationships to Specify at any time, but not all names in a Specify database need be represented by specimens in the collection catalog. New taxonomic names may be brought into the Specify taxon table through batch importation in an ITIS Taxonomic Workbench format file, or they may be entered one at a time through the taxon data entry form. For existing databases that we convert to Specify, we generate a taxonomic dictionary from your current determination data. Specify allows you to build the classification that is appropriate for your collection, using the names you prefer. Specify does not currently support multiple classifications (taxonomic trees), say for multiple users of the same specimen database.
How do I keep my Specify collection data secure?
Specify has a security system to administer user and group database permissions. Only users with Specify accounts may work with the database. There are five levels of Specify users ranging from Database Administrator to Guest. Each successive level has access to a subset of functions and rights. The administrator has all rights and may set the read and write access to each field for each lower category of user. For example, one could restrict Guests to read-only access of certain data fields.
Additionally Microsoft Windows Authentication for login and password security can be used to provide access to the Specify application. MSDE and SQL Server also have accounts and passwords which restrict access to underlying database from other applications.
The Specify web interface allows anonymous web access (no login required) and is read-only. The Specify database administrator can designate which fields and tables are exposed to Internet users.
Can I track changes to the database?
There are several ways to see what changes have been made to the database. One way is to view the LastEditedBy, TimestampCreated, TimestampModified fields for records in your data entry forms. This will allow you to determine who made changes to a record and when it was last changed (or first created). You may also filter query results to see only those changes made since a certain date. By retrieving the range of catalog records created in a data entry batch on a certain date or by a certain user, one could print out just those data for verification.
Can I tell who created a specimen record?
Viewing the LastEditedBy field of a newly created record will indicate the user name of the person who created it.
How do I backup my data?
Your Specify database is stored on a hard drive either in your workstation's MS SQL Server installation directory (which is the default location used by the Specify installation package) or on another machine acting as a database server. The initial configuration choices for Specify at your site, determine the location of your database. Specify 5 provides a simple menu option for creating a backup of your database and a corresponding restore utility. These backup files reside in the same directory as your database.
Alternatively, some institutions have server disks backed-up in their entirety by an independent process. A SQL Server installation on a department or institution server may also have its own separate backup schedule just for database files. Institutional system administrators should be apprised of your backup requirements and options, to be sure that backup procedures and schedules are well understood and adequate at your site.
We strongly recommend making daily backups of Specify databases to removable media, for on- and off-site storage.
How do I make my collection data available on the Internet?
Specify 5 includes a highly-configurable, robust web server interface. Database administrators are able to choose the fields exposed in web query pages. The format and style of web pages are customizable with style sheet controls.
Which web server does Specify work with?
Specify 5 is supported to run with the Microsoft IIS and with Apache running under Windows.
Can I track the activity of anonymous web users with my Specify database?
Yes, an easily-readable log of web queries and of the number of records returned from each query is maintained by the Specify web interface. It is viewable on the web. The web log also summarizes and ranks activities by various categories. Specify web logs are searchable by any specified start and end date period, and log entries can be exported to a file, such as a spreadsheet, for detailed analysis.
Can I change the query templates that are displayed in Specify's web pages?
Yes, Specify 5 has a capability for database administrators to create custom web query templates for Internet users. More than one pre-designed web query page can be exposed on the web site, perhaps customized for different projects or types of users. Specify makes the process of customizing web page layouts easy for someone with HTML template and style sheet experience.
Can I edit the HTML that generates Specify's web site?
Yes, you can modify the HTML page templates and the style sheets which work with them for outstanding customization capability.
Does Specify support DiGIR?
We include a DiGIR web service interface and installer for Specify collections to participate in biological discipline federations such as MaNIS, HerpNet, Fishnet, and also with global caches such the data warehouse of the Global Biodiversity Information Facility (GBIF). We plan to enhance Specify's internet interfaces for serving structured data in Release 6.
Do you have authority files for taxon names?
The first source for taxon names will be the determinations in your existing specimen data. If you do not have data to be converted to Specify, we can provide a classification of taxon records from the Integrated Taxonomic Information System (ITIS) database which emphasizes North American species. We are always looking for high-quality taxonomic data to share with the collections community. If you have data and would be willing to share it with colleagues in your discipline for collection cataloging uses, let us know, we'll convert it to a Specify format and make it available. Specify also includes functions for instant lookups on the online ITIS database of taxonomic names.
Do you have an authority file/pick list for geographic place names?
We include data entries from the Getty Thesaurus of Geographic Names within each Specify database.
Do you have pick lists for non-political place names, like rivers, and oceans?
Yes, many non-political names are included such as rivers, oceans and other water bodies.
What utility does Specify have for printing labels and reports?
Specify has a powerful report design and printing subsystem based on "Rave" software from Nevrona Designs. The report designer has outstanding flexibility for custom reports and labels of all sizes and layouts. The Specify Project offers free label and report design services for registered institutions.
Can I use my current printer with the program?
Specify works with any Microsoft Windows supported output device.
Can I print labels as I do now?
The Specify Software Project offers label and report template customization at no charge, based on your existing label and report formats. Advanced users will be able to create and edit report formats themselves. The Specify report designer allows you to concatenate data fields to produce paragraph-style descriptions of specimen information. Conditional logic is also supported for field labels, punctuation, etc. All installed Windows fonts are available in the report designer.
Can I print catalog pages?
Yes, you can print in any format. We have sample catalog pages to help you get started.
Can I print labels with bar codes?
Yes, we have several "symbologies" for bar codes.
Can I print tiny labels?
The smallest font Specify can print is 4 pt, the largest is 72 pt.
Are underlining and italics supported?
Yes, all Windows fonts and font features are supported.
Can I print specimen or lot labels for my collection on special paper?
Sure, this is not limited by Specify. You can print to any size stock or paper format.
Can I get a report of everything I have on loan?
One can run a query to determine which specimens are on loan and then print a report with the results.
Can I print a report of the number of specimens of a particular determination I have in my collection?
Yes, you can run a query on a particular name and then use a count field to produce the number of specimens with that determination.
Can I keep track of items on loan that do not have a catalog number?
Yes, Specify can "loan" specimens that are not individually cataloged in your collection, e.g. gifts for determination. By default, Specify tracks each individual cataloged item you loan or borrow.
Can I see which specimens are on loan, or those that have been deaccessioned?
An indicator in the record of the specimen indicates whether a specimen record has been loaned or deaccessioned. You can print a report of all specimens in either status.
If I have multiple specimens under the same catalog number, can I track which ones are on loan?
Specify will allow you to indicate the number of specimens on loan from a particular lot or container. As they are returned, you can indicate the number returned and the number still on loan.
Can I keep track of botanical specimen exchanges?
Yes, exchanges are tracked in a plus-or-minus tally. A positive number indicates the number of specimens you have sent to an institution, and a negative number those you have received.
Can I track partial returns?
You may indicate on the loan record which specimens from a particular loan have been returned.
Can I de-accession a specimen that was loaned and track it in the software?
Specify can de-accession specimens that were out on loan.
Can I trace the history of shipments?
Specify can report on the number of shipments sent out to a particular institution. It also keeps a record of who loaned each individual specimen.
Can I track the specimens that my institution has borrowed from other institutions?
Specify refers to such specimens as "Borrows" and keeps track of them. Borrows are not given catalog numbers and do not become part of your collection unless you accession them. This is a record-keeping feature that does not affect the contents of your primary collection database.
Can I track all the specimens that were brought in under one accession number?
Yes, if you label all of the specimens with that accession number.
Can I link permits to accession records?
Yes, permits and the people to whom they were issued may be tracked in an accession record and in individual specimen records as well.
Have another question? Please e-mail us: email@example.com
Last modified 2007-10-30 10:38 AM