Week 1
Developing a Protocol
for Scientific Collections
Natural History Institute, Prescott, AZ.
Senior Project- BS in Environmental Studies
Luna (Taide) Martínez G.
PRESCOTT COLLEGE
Spring 2014
Week 1
Luna (Taide) Martínez
Developing a Protocol for Scientific Collections
Basic theory, tools, and studies utilized to organize scientific
collections.
For this section, I will review a number of academic publications related to the
study of scientific collections, the processes utilized to digitize them, and their importance
in the field of conservation and biological inquiry. The goal of this initial literature search is
to provide the Senior Project with a theoretical foundation of some of the successful
practices applied to the development of protocols for natural history collections. Based on
this first approximation, I will be better able to evaluate and assess the strengths of software
appropriate for databasing material in the Natural History Institute. Finally, these reviews
will set a context for the creation of a data dictionary and a rubric to access available
biological software.
1. Digitization of Natural History Collections (Tegelber et al. 2012)
In this study, Tegerlber et al. (2012) describe an initiative to digitize natural history
collections in a Finnish museum of natural history using Darwin Core Archive. This effort
to increase productivity in the practice of digitization was established not only in order to
speed up the process, but also to provide a more effective service to museum customers via
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service packages. The steps of the process can be seen in the following model:
Spring 2014
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Luna (Taide) Martínez
Developing a Protocol for Scientific Collections
I will now describe some of the steps illustrated in the figure with the purpose of
considering how this digitization process could be applied to the NHI collections. As a side
note, I found that the datasets were described using metadata software such as Darwin
Core, and were stored in files using the Ecological Metadata Language EML, which was
described as a standard to describe datasets in the biodiversity science community (Fegraus
et al. 2005). This might be something to keep in mind when selecting software applicable to
the NHI collections.
-Receiving: This step involves some handling of specimens; it is important,
however, to determine criteria to select material for digitization based on the NHI own
prioritization process.
-Tagging: This step involves handling of the specimen as well. Each sample would
be tagged with a label, which generally contains a unique identifier. The label could also
include an HTTP URI. Prior to establishing a Data Dictionary for the NHI, the field names
to be used would have to be determined.
-Imaging: The specifics of this step depend on the type of specimens to be digitized.
Both the specimen and its label would be digitized.
-Delivery and specimen repository: Some museums handle and digitize specimens
that belong to other collections, but which can be incorporated into their own digital
database. The NHI could either borrow specimens stored by a third party or store them
temporarily along with its collections.
-Data entry: Data from the labels are entered manually from the images using the
vocabulary of the data exchange standard of our chosen software. I found that Finnish
museums tend to use Darwin Core.
-Georeferencing: Geographic coordinates could be available for some specimen
-Filtering and validation: Some details, like coordinates of endangered species
locations, could be filtered before publishing the digitized data. Finally, a check of the data
entry should be made before releasing information.
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labels. Web services such as GeoLocate could be used to retrieve them automatically.
Luna (Taide) Martínez
Developing a Protocol for Scientific Collections
-Publishing: The collection data would then be imported to the database service and
made available to people. In Nordic countries, the Morphbank service seems to be widely
used as a database tool for natural history specimens. There is also an Integrated Publishing
Toolkit online that hosts biodiversity data to be shared globally.
2. Industrial Scale Digitization of NHC (Blagoderov et al. 2012)
This article presents methods for a large-scale and coordinated process of
digitization of natural history collections. By some estimates (Ariño 2010), only about 3%
of specimen data from NHC in the world is available online through the largest web source
of
biodiversity
information,
Global
Biodiversity
Information
Facility
(GBIF;
http://gbif.org/). This is partly due to the large amount of data in these collections and the
lack of human, economic, and time resources to digitize them. According to Blagoderov
(2012), this process could take as long as 1,500 years and cost up to $200 billion USD. One
of the author’s suggestions to address this issue is focusing on selective digitization goals
based on standardized large-scale criteria such as:
-An automated procedure in all steps that do not require handling of specimens.
-Digitization of entire collections instead of selected specimens.
-Steps that require handling could be systematized, for example by assigning
specimen labels simultaneously to all specimens in a group.
-Standardizing metadata collection (i.e., specimen location in the collection, unique
ID, etc.). This could involve, for example, labels with a human-readable number and a
machine-readable barcode as well.
These suggestions could streamline the process of digitizing a whole NHC and
providing readily available public access to them. Before determining what protocol to
approximately 90% of the time required for digitization is spent on capturing metadata and
labeling specimens. However, this work could also be performed by trained volunteers of
work-study staff, who would gain the additional benefit of learning a new set of skills.
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kind of data we determine to be necessary in the labeling and data entry process, since
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establish as a baseline for the institute’s collection, perhaps it is important to consider what
Luna (Taide) Martínez
Developing a Protocol for Scientific Collections
3. Creating Herbaria and Natural History Collections (Snow 2005)
In this article, Snow explores the contributions of small herbaria and natural history
collections to academia and society in general. He recognizes, on the other hand, that these
institutions often lack personnel to assist with management of the collections. He proposes
a few solutions to deal with this problem, such as strengthening communication channels
from the facility within and outside the institution in order to ensure its long-term viability.
Among the benefits that small natural history collections provide to society and
which seem compatible with the Natural History Institute, I found:
-Supporting students and faculty in research of regional biodiversity.
-Using the collections within a course setting to strengthen the experiential nature of
the teaching/learning experience.
-Providing training for students interested in curatorial studies and biodiversity
research.
-Integrating the objectives of different disciplines and projects within and across
academic programs.
-Streamlining communication and linkage between student projects and other
universities, nonprofit organizations, and government sectors relevant to the project.
-Providing global access with information about local biodiversity and taxonomy by
entering specimen labels into online databases.
-Exchanging specimens on loan with similar institutions in order to expand the
academic and research offerings of the institute.
the long-term goals of the NHI.
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-Providing Senior Project and Independent Study opportunities that would benefit
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-Becoming a center for researchers to access resources of regional biodiversity.
Luna (Taide) Martínez
Developing a Protocol for Scientific Collections
-Providing education to the Prescott community by offering hands-on access to
collections.
-Creating volunteer opportunities for students.
The NHI also derives its importance from the potential possession of a collection
that, however small, would not be duplicated by other regional institutions. In this way, and
in line with Snow’s perspective, it can become a repository of public information and
outreach on environmental issues in general. However, it is important to look at similar
collections in size and nature and identify the difficulties they have faced over time in order
to install preventative measures and be prepared to face them as they arise. I have found
that a lot of small collections are often incompletely curated and a large proportion of its
specimens are unprocessed and undigitized. For this reason, I find my senior project and the
current research on database and collection management software important in their
contribution to the NHI’s goals. Establishing operational protocols for existing and
incoming specimens early in the development in the institute is crucial in ensuring that the
collection as a whole has digital reference materials and is up-to-date with database design
standards utilized globally.
A Collections Management Handbook will be an important tool to secure this goal.
Future staff might not be trained or have experience working in similarly sized or larger
collections. Developing a clear protocol for the preparation, label making, and data entry of
specimens is essential to prepare for future curatorial management. The initial
establishment of an active institute will require investment of time from part of the NHI
staff and volunteers. It seems like developing an operational budget, either annual or with
multi-year projections, is important in the early stages of the institute as well. According to
this article, a budget similar to ours ($3500) would allow an active herbarium of 30,000
specimens.
could be helpful to monitor the institute’s progress and could be used as part of grant
proposals in the future. Most database grants require databases to comply with certain
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exchanges, and internal movement of species. Annual summaries of activities and progress
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Additionally, the NHI could consider establishing a protocol to track loans,
Luna (Taide) Martínez
Developing a Protocol for Scientific Collections
globally accepted standards and to provide georeferencing of specimens. Considering this
when selecting the database program and operating system to use might be important.
Likewise, some databases could be easily convertible into a different format in order to use
another program in the future, even though I would personally prefer to adopt a given
program and retain it. Finally, database management seems to follow a learning curve that
we should take into account when hiring work-study positions or involving volunteers. I
found that when a database becomes available online, the workload of maintaining its
functionality also increases. These are some resources that we might want to explore as part
of that process:
-ABCD Schema (Task Group on Access to Biological Collection Data);
www.bgbm.org/TDWC/CODATA/Schema/default.httn
-BioCASE (Biological Collection Access Service for Europe): \vvirw.biocase.org
-Darwin Core 2: http://darwincore.calacadetny.org
-Distributed Generic Information Retrieval (DiGIR): http://digir.sourceforge.net
-Global Biodiversity Information Facility (GBIF):\\rww.gbif.org
-HerpNET: www.herpnet.org
-Index Herbariorum: http://sciweb.nybg.org/science2/IndexHerbariorum.asp
-Mammal Networked Information System (MaNIS): http://elib.cs.berkeley.edu/manis/
-Ornithological Information System (ORNIS): http://ornistiet.org
-Taxonomic Databases Working Group (TDWG):wvirw.tdwg.org
According to Snow’s article, many small facilities lack enough funding to support a
full-time position for a staff involved in curating the collection. I am unaware of whether
there is a clear time allotment devoted to curation alone in the job description for the NHI’s
staff, but collections smaller than 50,000 specimens seem to devote about 30 percent of
their time to this activity. Snow also recommends close monitoring of all visits to and uses
of the facility’s collection and space, since this can be included in annual reports.
Establishing communication and alliances with nearby facilities like we have done with
Yavapai College, and strengthening linkages within the supporting institution, in this case
Prescott College, be it with undergraduate and graduate students, faculty, or staff. Finally,
source of knowledge about life on Earth that they provide. In regions like the Southwest,
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long-term monitoring of ecosystem composition and changes can provide important insight
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this article explores the importance of natural history collections in general in terms of the
into the effects of threats such as global environmental change. This information could then
be applied to conservation efforts and be used as part of policy decisions.
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Luna (Taide) Martínez
Developing a Protocol for Scientific Collections
4. The Importance of Natural History Collections and Herbaria
(Nelson et al. 2013).
This article explores the historical importance of establishing and maintaining
facilities like the Natural History Institute. NHC serve as reference for regional specimens
and provides insight into the distribution of biodiversity in space and time. Providing
researchers with access to these resources allows them to document and analyze
relationships between and among species as well as the effect of environmental changes on
their distribution and population dynamics. Furthermore, biological science research often
depends on testable and repeatable hypotheses that can rely on taxonomy and registered
specimens. In an era increasingly threatened by anthropogenic changes to the biosphere,
these archives of life on Earth have important applications in the fields of ecology and
conservation biology (McCarthy 1998), for example, by predicting future changes in
species ranges and richness.
According to this article, it is important for managers of scientific collections to
ensure that all data associated with specimens provide the same type of details and are
consistent in their format. The NHI can be a catalyst for more active research and data
collection in the region, and could provide basic training for undergraduate students with
interest in engaging with this kind of practices. As a consequence, the level and standard
used for identification, recording, and data collection would be consistent, improving the
quality of the institute’s records. Collecting specimens in a systematic and targeted way for
specific research purposes could provide a great opportunity for senior projects and
independent studies, while contributing to the collection of the NHI. By establishing
development policies for this facility in its early stages of development, we could identify
opportunities for applications for environmental and conservation science, as ell as research
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on biological systematics and taxonomy.
Spring 2014
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Luna (Taide) Martínez
Developing a Protocol for Scientific Collections
5. The Legacy of NHC (Dunnum and Cook 2012)
This article explores the evolution of the role that NHC have played in our
understanding of the natural world. I believe that it is relevant to my senior project because
it places into context the work and potential application of the NHI, as well as the
importance of establishing a protocol and a database for its collections. The article provides
insight into the history of establishing scientific collections and the development of
catalogues across time. The progress of technological advances now allows these
collections to be preserved in more perpetuity than before and to be available to the
scientific community a large. However, the physical collections themselves provide
historical baseline conditions that would otherwise be difficult to obtain. Coupled with the
use of climate models, addressing potential responses to global environmental changes by
regional biodiversity is now easier than ever before.
An important reflection of the article analyzed the development and formalization
of standards of operation for scientific collections. Gerrit Miller is cited as one of the great
predecessors of systematic and curation, developing some of the standards we use today in
terms of data collection, entry, and nomenclature. Understanding the legacy of these early
researchers can help to recognize the most widely-accepted methods to record and
systematize information in scientific collections. Communication technologies can today
allow for cross-disciplinary contributions and perhaps mitigate the detrimental impact of
human actions on the environment. Furthermore, the NHI can be a pillar for community
education by exposing new generations to the region’s biodiversity through collected
specimens.
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Arino AH (2010) Approaches to estimating the universe of natural History collections data.
Biodiversity Informatics 7: 81–92.
Blagoderov, V., Kitching, I.J., Livermore, L., Simonsen, T.J., Smith, V.S. 2012. No
specimen left behind: Industrial scale digitization of natural history collections.
Zookeys 209: 133-146.
Dunnum, J.L., Cook, J.A. 2012. Gerrit Smith Miller: his influence on the enduring legacy
of natural history collections. Mammalia 76(4): 365-373.
Fegraus EH, Andelman S, Jones MB, Schildhauer M (2005) Maximizing the value of
ecological data with structured metadata: An introduction to Ecological Metadata
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Literature Cited
Luna (Taide) Martínez
Developing a Protocol for Scientific Collections
Language (EML) and principles for metadata creation. Bulletin of the Ecological
Society of America 86 (3): 158–168.
McCarthy MA (1998) Identifying declining and threatened species with museum data.
Biological Conservation 83: 9–17.
Nelson, W.A., Dalen, J. Neill, K.F. 2013. Insights from natural history collections:
analyzing the New Zealand macroalgal flora using herbarium data. Phytokeys 30:121.
Snow, N. 2005. Succesfully curating small herbaria and natural history collections in
academic settings. BioScience 55(9):771-779.
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Tegelberg R., Haapala J., Monone T., Pajari M., and Saarenmaa Hannu. 2012. The
development of a digitising service centre for natural history collections. Zookeys
209: 75-86.
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