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Arctos
Arctos
Multi-Institution, Multi-Collection Museum Database
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Arctos is an ongoing effort to integrate access to specimen data, collection-management tools, and external resources on the Web. Nearly all that is known about a specimen can be included in Arctos, and, except for some data encumbered for proprietary reasons, data are open to the public.

Features:

  • Vaporware-free since 2001. All this stuff, and much more, really exists in a usable state, and we'll never claim proposed or limited funtionality exists.
  • Media links images, moves, sound files, and documents to specimens, taxonomy, publications, projects, events, or people.
    Multi-page documents organize, paginate, and print PDFs of scanned media such as field notes.
    TAGs comment on specific areas of images, or relate them to nodes such as specimens, places, and people.
  • Users may annotate specimens, taxonomy, projects, publications, and media.
  • Virtual Private Databases (VPD), also known as Row-Level Security (RLS), allow collections to maintain control of their data while sharing certain nodes, such as Agents and Taxonomy. The cool kids call this Cloud Computing or Grid Computing. It allows us to confidently support most any application, not just the ones we write.
  • Everything is over the web in real time, and independent of client-side operating systems. You need moderate bandwidth, a modern browser, and nothing more.
  • Specimen-search screen is user-customizable to about 100 search terms. Find specimens by project, publication, usage, taxonomy, spatial attributes, and much more. Save and e-mail searches.
  • Customizable table for result sets, summarize and graph result sets, download (as text, CSV, or XML), map in BerkeleyMapper, Google Maps, or download KML for Google Earth.
  • Customizable by individual collection using headers and footers of their own design, and CSS.
  • Any cataloged item can have any number of attributes, and attributes are customized to collections.
  • Reciprocal linkages with external resources (BerkeleyMapper, GenBank, TACC, and MorphBank).
  • Identifications can be formulaic combinations of terms drawn from a separate taxonomic authority.
  • Maintains history of determinations for taxonomic identifications, georeferencing, and biological attributes.
  • Specimen records, specimen parts, attributes, citations, and much more can be entered or edited individually or in batches.
  • Object-tracking using nested-containers model, bar codes, and container-condition history.
  • E-mail reminders for loans due, permit expirations, etc. Intelligent reports detailing possible GenBank matches, missing citations, unlikely publications, and various other potentially faulty or missing data. more information
  • Encumbrances can mask localities, collector names, or entire records from unprivileged users.
  • Design and print labels, reports, transaction documents, etc. with a GUI interface.
  • Arctos is a DiGIR provider.

Nodes

Arctos may be thought of as a number of overlapping nodes.

  • Specimens are the core of Arctos. Traditional museum "label data" lives here. Attributes allow collection-specific determinations of most anything that can be recorded from a specimen, such as sex, weight, age, and various measurements. Specimen Parts are the physical objects, and are grouped as Cataloged Items, which represent one or more biological individuals. Cataloged items may be encumbered in order to restrict access to objects or data. Other Identifiers record any number assigned to a specimen, and may form links to external resources such as GenBank.
  • Containers hold specimen parts and other containers in a flexible recursive model. Containers may be barcoded. Some containers hold fluid, and record a history of concentration and monitored dates. All containers maintain a position and condition history.
  • Transactions consist of loans, accessions, and borrows, and may be grouped through projects.
  • Localities record descriptive spatial and coordinate data, along with collecting methods, habitat, and dates.
  • Agents are people, groups, or organizations that collect specimens, determine identifications, attributes, and coordinates, create, authorize, and participate in tranactions, author publications, and act in various other roles.
  • Publications are attached to specimens by way of citations, and are often created by projects.
  • Projects create and use specimens, produce publications, group taxonomy into checklists, and record usage of speciemns in the absence of formal citations.
  • Taxonomy forms the basis for identifications and citations. Taxa may be related to each other, and to any number of common names in any language.
  • Media attaches digital resources to specimens, people, places, and publications. TAGs graphically reference images to specimens, places, and people. Documents paginate scanned publications, such as field notes.

Participation
Arctos is currently two systems sharing the same code. One is a multi-hosting version that includes collections at the University of Alaska Museum of the North, the University of New Mexico's Museum of Southwestern Biology, Western New Mexico State University, and the Museum of Vertebrate Zoology. A second server at the Harvard Museum of Comparative Zoology hosts MCZ's Herp collection, with more collections coming soon.

Arctos is rooted in the Collections Information System at MVZ. Development efforts are shared, and programming is freely available.

Collections or institutions interested in having their data hosted in Arctos, or interested in participating in the development of Arctos should review the participation guidelines, then contact us for additional information.

System Requirements
We attempt to keep the client-side of Arctos applications as generic as possible, but we have made some exceptions:

  • JavaScript: We have used JavaScript throughout the applications. Your browser must be JavaScript enabled to access all the features of such applications.
  • Cookies: We use cookies only to set and preserve user preferences and user rights. In order to benefit from all but the most basic public features, you must enable cookies.
  • Popups: Users may wish to enable popups. Some informational windows use popups. We promise to only pop up things you ask for.
    Operators must enable popups. Many browsers block this, sometimes cryptically, by default.

Browser Compatibility

  • Mozilla Firefox: All applications have been tested in Firefox. We highly recommend all users upgrade to the latest release of Firefox, available from Mozilla.
  • The Rest: Most of Arctos should work most of the time in most other browsers. Let us know if you have trouble accessing this site in your browser, and we'll fix it if we can.

Data Usage
The collections data available through Arctos are separately copyrighted © 2001 - 2009 by the University of Alaska Museum of the North (University of Alaska, Fairbanks, AK), and by the Museum of Southwestern Biology (University of New Mexico, Albuquerque, NM), and the Museum of Vertebrate Zoology (University of California, Berkeley, CA). All rights are reserved. These data are intended for use in education and research and may not be repackaged, redistributed, or sold in any form without prior written consent from the appropriate museum(s). Those wishing to include these data in analyses or reports must acknowledge the provenance of the original data, notify the appropriate curator, and should ask questions prior to publication. These are secondary data, and their accuracy is not guaranteed. Citation of Arctos is no substitute for examination of specimens. The data providers are not responsible for loss or damages due to use of these data.

FAQ

Q: Are these live data?
A: Almost. Live data are stored in a highly normalized relational structure - fabulous for organization, not so hot for query. Some data are then optimized for query performance by way of Database Triggers. Presentation data are generally less than one minute stale.
Q: Is there a limit on the number of records I can return in a search?
A: We impose no strict limits. Queries almost always take less than 5 seconds. Getting the data to your browser often then becomes a bottleneck. If you have a reasonably fast browser and connection, it should be possible to return at least 100,000 basic records with a single query. We have no idea why you'd want to. Let us know if you find something excessively slow.
Q: What's a VPD?
A: A Virtual Private Database allows us to share resources, like programmers and hardware, along with some data, such as Taxonomy and Agents. We all end up with more than we could afford by ourselves, and operators generally can't tell that they're in a shared environment.
Q: What's Media? Can I store images or video in Arctos?
Media, loosely defined, is anything you can produce a URI for. Web pages, Internet-accessible images, and documents stored on FTP sites are all potentially Media. Media may form relationships with any "node" in Arctos.
Arctos proper offers little in the way of storage. However, we have a partnership with the Texas Advanced Computing Center which provides us access to essentially unlimited storage space. Arctos currently links to around 10 terabytes of Media, primarily high-resolution images of ALA herbarium sheets and historical MVZ images, both on TACC's servers.
Q: Why Oracle and ColdFusion?
Because they work. We've tried many other solutions along the way. Oracle is rock-solid and stable, and allows us to do things like share/control data via VPDs, maintain current data to our query environments, and sleep at night. ColdFusion is a very robust rapid development environment that fits our programming style perfectly while providing very close to 100% uptime and reliability. On a more practical level, implementing an open-source solution would necessitate hiring at least one additional person to mange software, while compromising stability and security.
Q: How does Arctos compare with Specify?
While sharing a common ancestor, Arctos and Specify now differ almost every level - software, hardware, security model, data model, development strategy, and support community. A comparison is available.
Q: What about security and backups?
Arctos has multiple levels of security. A lightweight application security package controls access to forms, while Oracle partitions data by user, roles, and context, and provides auditing. Incremental backup logs are maintained on mirrored disks, and daily backups are maintained in 3 geographically separate secure locations.

Suggestions?
The utility of Arctos results from user input. If you have a suggestion to make, let's hear it. We accommodate many special requests through custom forms or custom queries, and many of these are then incorporated into Arctos. Please contact us if you have any questions, comments, or suggestions.

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