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A Collaborative System for Sharing Paleontology Collections Data

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A Collaborative System for Sharing Paleontology Collections Data A collaborative system for sharing paleontology collections data Kenneth G. Johnson1 Harry F. Filkorn Mary Stecheson Department of Invertebrate Paleontology, Natural History Museum of Los Angeles County, 900 Exposition Boulevard, Los Angeles, California 90007, USA ABSTRACT and physical sciences, and they represent it has been clear that the World Wide Web is one way forward into a data-rich future for an ideal forum to publish collections catalogs. Museum collections provide primary paleontology. Besides widespread availability and ease of data for paleontologists, and recent advanc- access, the Internet offers the additional ben- es in information technology have revolu- Keywords: geoinformatics, paleontology, e®t of allowing databases to be integrated into tionized how museums collect and share collections. new networks of bioinformatics and geoinfor- this information. However, many natural matics (Graham et al., 2004). Such networks history museums have huge collections and INTRODUCTION enable researchers to address questions re- small budgets, so museum scientists are garding the large-scale history of regional or challenged to keep these critical data cur- Fossil specimens are the best record of the global diversity in response to global environ- rent and available to the public. We suggest occurrence of a particular organism at a spe- mental change (e.g., Jackson and Johnson, that establishing an open collaboration ci®c time and place (Allmon and Poulton, 2000; Alroy et al., 2001), and are an inevitable through the Internet is one possible solution 2000), so collections are the raw data of pa- part of the future of paleontology. to this challenge. To achieve this solution, leontology. Collections are required for sub- Most natural history collections belong to we have implemented a Web-based collec- sequent researchers to check and reinterpret public or nonpro®t institutions that hold their tions catalog to encourage collaborative previous work, and they are an important collections in the public trust (American As- maintenance of collections data as a shared source of new information that can be released sociation of Museums, 2005). However, many resource. Anyone can search the catalog via by the arrival of new technologies and new of these institutions have recently been subject a simple interface designed for any stan- research questions. For example, collections to budget shortfalls (Dalton, 2003; Suarez and dard Web browser, and Web users can also have been used in studies based on morpho- Tsutsui, 2004) that have reduced support for be authorized to add information or update metric analysis, molecular methods including collections. At the same time, changing or- DNA sequencing, and various geochemical records as stratigraphic and taxonomic ganizational priorities has resulted in the techniques (Suarez and Tsutsui, 2004; All- concepts change. The goal is to establish transfer of collections to a smaller number of mon, 2005). Collections held by museums be- two-way communication between our cata- institutions (Gropp, 2003). For example, the come especially important in cases where log and the scienti®c community wherein Department of Invertebrate Paleontology at the museum shares its collections and re- original exposures are no longer available for the Natural History Museum of Los Angeles lated data, and in return the community collecting, as is commonly the case for man- County (LACMIP) currently contains collec- contributes new data acquired through use made exposures produced during road build- tions that formerly belonged to the University of the collections. The catalog also provides ing, quarrying, or construction. However, col- of Southern California, the University of Cal- a basic function for building links with on- lections of fossils are only useful if they are ifornia at Los Angeles, the California Institute line publications and other data sources. As accessible to potential users. Traditional use of of Technology, and California State Univer- data exchange standards become accepted, paleontology collections required researchers these links can be used to create metada- to visit museums and work with material on- sity, Northridge. The consequence of these tabases that could lead to global networks site or resort to secondary sources in the pub- transfers is that relatively small staffs are car- of collections, taxonomic, stratigraphic, and lished literature. In reality, much of the infor- ing for many large and important collections bibliographic information. By providing an mation about the contents of paleontology that are critical to the future of paleontology. ef®cient mechanism to locate and synthesize collections is passed along by word of mouth, Besides limitations in manpower, there is an large volumes of disparate information, as a kind of folklore: for example, Heinz Low- increasing shortage of expertise. With reduced such loosely integrated systems have result- enstam was a professor at the California In- staff, most institutions do not have in-house ed in rapid progress in disciplines of the life stitute of Technology, so his collections might experts that can serve as taxonomic authorities be held by an institution in Southern Califor- in the entire spectrum of fossil groups repre- nia. Obviously, this is not the most ef®cient sented in their enormous combined collec- 1Current Address: Department of Palaeontology, Natural History Museum, Cromwell Road, London method to advertise the availability of impor- tions. Without this expert knowledge in-house, SW7 5BD, UK. tant research collections. For at least a decade, it is dif®cult to adequately maintain and im- Geosphere; October 2005; v. 1; no. 2; p. 61±77; doi: 10.1130/GES00011.1; 7 ®gures. For permission to copy, contact [email protected] q 2005 Geological Society of America 61 Downloaded from http://pubs.geoscienceworld.org/gsa/geosphere/article-pdf/1/2/61/3332304/i1553-040X-1-2-61.pdf by guest on 02 October 2021 JOHNSON et al. Figure 1. An example of a specimen lot from the Department of Invertebrate Paleontology at the Natural History Museum of Los Angeles County (LACMIP) collections, including paper labels containing potentially useful information that should be incorporated into the LACMIP specimen catalog. prove collections without enlisting the support the Great Basin or Pleistocene mollusks of ued access to high-quality information. Other of experts in the broader paleontological com- western North America. Collections managers ®elds of research within bioinformatics are munity. This outside assistance must come provide free access to specimens and data, but reaching the same conclusion (Eiden, 2004; from the researchers using museum collec- sharing must become a two-way street. The Wilson, 2005). To help achieve this, we have tions to address questions in their own spe- research community using these resources developed a Web-based collections catalog cialized ®elds, whether Cambrian trilobites of must contribute its expertise to ensure contin- that can be jointly managed by the museum 62 Geosphere, October 2005 Downloaded from http://pubs.geoscienceworld.org/gsa/geosphere/article-pdf/1/2/61/3332304/i1553-040X-1-2-61.pdf by guest on 02 October 2021 SHARING PALEONTOLOGY COLLECTIONS DATA Figure 2. A schematic model illustrating the architecture underlying the Department of Invertebrate Paleontology at the Natural History Museum of Los Angeles County (LACMIP) catalog. All information is stored in a relational database and is accessible through four user interfaces. Web forms and REST-style Web services can be used to search, browse, and add information into the system. Software underlying each component is indicated in parentheses, including Apache Web server, PostgreSQL database management system, and SQL and PHP programming languages. Connections between Web server and clients on the World Wide Web can be encrypted using the modpssl module available with the Apache Web server software. collections staff and research community as a that have been identi®ed as belonging to the the late 1980s these data were entered by hand shared resource. same taxon. Over the years, each lot may have into a custom collections management system The LACMIP holds more than ®ve million accumulated a group of paper labels that con- developed in Borland Paradox. Nontype spec- specimens, primarily from the western United tains information regarding the fossil collect- imens that had never been ®gured in publi- States, including the world's largest collec- ing locality and sometimes multiple taxo- cations were not cataloged. However, the card tions of Cretaceous and Neogene mollusks nomic determinations made by different system continued to be maintained in parallel from western North America. Our collections researchers who have studied the material. For with the computer database and was consid- have been built over the past 90 yr and include example, the gastropod illustrated in Figure 1 ered the standard. In 2002 we extracted the the important university collections mentioned has four different hand-written and typed la- data from the legacy database and reformed it above that were transferred to the museum as bels that contain such data. One of our chal- into a new system. local universities decided to eliminate their re- lenges is to capture these data and make them search collections. The department is currently available to the public. THE LACMIP COLLECTIONS housed in an off-site facility about a half mile Cataloging of the collection
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