FINAL REPORT,
INVENTORY OF BIODIVERSITY
DATABASES IN
Prepared for
By
Allegheny Institute
of Natural History,
The Pennsylvania Biodiversity Partnership’s Biodiversity Metadata Form can be viewed at URL:
http://www.upb.pitt.edu/ainh/metadata/index.htm
(PBP’s Biodiversity Metadata Form on the web was renamed “Biodiversity Data Description Form” after receiving suggestions from the Concurrent Session 3: Biodiversity Information at the annual PBP conference, November 30, 2001, to make the form sound more “user-friendly.” Throughout this report, however, I will continue to refer to “metadata” and the “biodiversity metadata form”.)
Before developing the metadata form, I did a web search
(Pennsylvania Spatial Data Access, PASDA; National Biological Infrastructure;
National Spatial Data Infrastructure; Federal Geographic Data Committee; United
States Geological Survey, USGS; Global Biodiversity Information Facility;
Global Change Master Directory, GCMD; and Association for Biodiversity
Information); personally met with metadata compilers (Maurie Kelly and Chris
Pfeiffer at PASDA); and corresponded by email and/or spoke to several metadata
experts in the field by phone (Anne Frondorf, Biological Data Working Group,
USGS; Sharon Shin and Susan Stitt, Biological Resources Division, USGS; Cheryl
Solomon, NASA, GCMD; and Peter Schweitzer, metadata tools, USGS) to determine
if there was a standard form for collecting biodiversity metadata. Cheryl Solomon posed the question to her
network of metadata compilers, and forwarded their input to me. I evaluated several forms currently in use
throughout the
The PBP Biodiversity Metadata form was developed using
nationally accepted metadata standards for biological data profiles (Biological
Data Profile, Biological Data Working Group, Federal Geographic Data Committee,
National Spatial Data Infrastructure) and adapted for use in gathering
The request for biodiversity metadata was sent via email to individuals, organizations, and agencies, both public and private, who were identified as being potential holders of PA biodiversity datasets. Requests for biodiversity metadata were sent to: members of PBP; state governmental agencies; federal agencies, including the USDA US Forest Service Warren Forestry Sciences Laboratory and Allegheny National Forest offices in Warren; museums; arboreta; Pennsylvania college and university biologists, ecologists, and environmental biologists; nature organizations, including conservancies, Audubon groups, regional conservation and watershed groups; and private landholders.
The request briefly described PBP. It explained that we were requesting biodiversity metadata to include in a “state of the state” PA report, and that the report would serve as a guideline for developing a biodiversity conservation plan for the Commonwealth. It explained that we were looking for both specimen-based and ecology-based datasets of PA’s biota, in any format. The request included directions and a link to the PBP Biodiversity Metadata website: http://www.upb.pitt.edu/ainh/metadata/index.htm . The URL also includes background information on PBP. The request emphasized that PBP was asking only for a description of the dataset and not access to the data. Those with no datasets were asked to submit a “no metadata to report” form.
We requested that
addressees forward the message to colleagues who maintain biodiversity
datasets. We also noted the projected
completion date of the "state of the state" report in early 2002 and
that the report, including a directory of
Contact information
was included: If you have any
questions or comments about this project or would like additional information
about PBP, please feel free to contact me (severson@pitt.edu) or
More than a thousand original requests were sent. Follow-up requests were also sent to PBP members and to known large dataset holders who had not yet responded. The text of the first and repeat message follows:
Header: PA Biodiversity Metadata Form
To: Biodiversity Experts and Stakeholders
From:
Re: Request for Information on
The
conservation
plan. As part of this "state of the
state" effort, we are compiling a directory of databases in
If you have one or
more specimen-based or ecological datasets of
Metadata
Form". PLEASE NOTE, we are NOT
asking for access to your datasets. We
are requesting a DESCRIPTION ONLY of your existing datasets. In so far as possible, we have developed a
biodiversity metadata form in keeping with national standards for the
collection of biological metadata. The form has been tailored specifically to
the needs of PBP.
If you DO NOT have a
specimen-based or ecological dataset, please go to
http://www.upb.pitt.edu/ainh/metadata/index.htm and click on "No metadata
to report? Click here".
If you know of a
colleague who maintains a specimen or ecological biodiversity dataset, please
feel free to forward this message to them.
The projected date of
completion of the "state of the state" report on biodiversity is
early 2002 and information compiled for that report, including a directory of
Pennsylvania biodiversity datasets, will be made available through the PBP
website (under construction). Background
information about PBP
is included on the URL for the metadata form.
If you have any
questions or comments about this project or would like additional information
about PBP, please feel free to contact me (severson@pitt.edu) or
Thank you for your
valuable assistance,
In addition, after the annual conference, and as a result of feedback from the concurrent session on Biodiversity Information, a new request was drafted. It was more “user friendly”; i.e., it eliminated the term “metadata” and briefly described the types of data that would be of value to PBP in developing a biodiversity conservation plan for PA. It was sent to all who received the original mailing and also to all PBP Annual Conference attendees. The message follows:
Header: help PBP
conserve PA's biodiversity
To: PA Biodiversity Experts and Stakeholders
From:
Re: Request for Information on
Do you have a teaching
collection of plants and/or animal specimens?
Have you been monitoring squirrel foraging habits in an
If you have been
collecting this kind of information, would you be willing to let other
researchers in PA know about your work?
If so, please go to http://www.upb.pitt.edu/ainh/metadata/index.htm
click on "Biodiversity Data Description Form" fill out and submit a description of the data
you have been collecting. If you reply
by
PLEASE NOTE, we are
NOT asking for access to your datasets.
We are requesting a DESCRIPTION ONLY of your existing datasets--whether
they are in field notes or
electronic format.
If you DO NOT have a
specimen-based or ecological dataset, please let us know that, too. Go to http://www.upb.pitt.edu/ainh/metadata/index.htm
and click on "No Biodiversity Information to Report"
If you know of a
colleague who maintains a specimen or ecological biodiversity dataset, please
feel free to forward this message to them and encourage them to participate.
If you have any
questions or comments about this project or would like additional information
about PBP, please feel free to contact me (severson@pitt.edu) or
Thank you for your
valuable assistance,
PS: The Pennsylvania Biodiversity Partnership
(PBP), a public-private partnership, formed to advance biodiversity issues in
Pennsylvania is presently preparing a report on the current state of
biodiversity in Pennsylvania as the first step in developing a statewide
biodiversity
conservation
plan. As part of this "state of the
state" effort, we are compiling a directory of databases in
A list of names/organizations/agencies/groups and email addresses is included in the appendix in an MS excel file entitled “metadata list”.
Requests (and reminder requests to those most likely to hold large datasets) for biodiversity metadata were sent to:
Members of PBP Directory of 10-01 |
|
PNDI |
Selected Register of PA Biologists. 1992 |
The Nature Conservancy |
Selected DCNR, PFBC, and PGC reps in Linking PA’s Ecological Databases, Bacastow et al. 1999 |
|
Organismal biologists & ecologists at all of PA’s colleges & universities |
DCNR (Dept of Conserv & Natural Resources) |
|
Bureau of Forestry: Science Office and District Foresters |
USDA Warren Forestry Sciences Lab Main ANF offices |
PGC ( |
Watershed Associations |
PFBC (PA Fish & Boat Commission) |
PINBIOP (PA Invert Biodiversity Project) |
DEP (Dept of Environmental Protection) |
PASDA ( |
Groups in DEP’s PA Conservation Directory |
PBP’s RFP consultants |
Carnegie Museums Curatorial staff of the various departments |
Curatorial staff of the various departments |
Morris Arboretum |
Frost Entomological Museum |
|
|
PBP Annual Conference Attendees |
|
|
TAXACOM listserve |
One hundred eighteen respondents described their biodiversity databases. Forty-one respondents had no biodiversity data to report. The total response rate to the survey was about 15%. Eleven% had biodiversity metadata and 4% did not.
In addition, Thomas Ford, Pennsylvania Fish and Boat
Commission, provided the data of the 1999 Bacastow, et al, study, (Executive
Report Linking Pennsylvania’s Ecological Databases of the Pennsylvania
Department of Conservation and Natural Resources, Fish and Boat Commission, and
Game Commission by Bacastow, Todd S., Maurie C. Kelly, and Ryan E. Baxter,
August 1999.) in hard copy and electronic format, and it is included as part of
this report as auxiliary materials. One
hundred nine reports were included in this study commissioned by the
Pennsylvania Department of Conservation and Natural Resources (DCNR), Fish and
Boat (PFBC) and Game Commissions (PGC) to study the feasibility of linking
It appears that the only overlap in the two surveys is part
of the PNDI database. PNDI is a cooperative
partnership of the Department of Conservation and Natural Resources’ Bureau of
Forestry, The Nature Conservancy, and the Western Pennsylvania Conservancy. PNDI filled out PBP metadata reports for
their databases of special concern vertebrates, invertebrates, and plants. Metadata for the Bacastow et al report is of
their entire database, which is a site specific information system that
describes significant natural resources of
One hundred and eighteen metadata forms have been submitted
as of
We have heard from many of the identified large biodiversity
database holders in
Botany--Bryophytes
Botany--Vascular plants
Ichthyology
Ornithology
Mycology
Invertebrate Paleontology
Amphibians & Reptiles
Bird Banding
Birds
Mammals
Vascular Plants
DEP—aquatic and terrestrial insects
Morris Arboretum—vascular plants
PNDI—East, West, Central
Special Concern
Invertebrates
Vascular plants
PNDI—East
Special Concern Vertebrates
PNDI is still working on its “negative database”; i.e., its very large biodiversity database of organisms and natural communities that are not of special concern, and will submit metadata when it is feasible for them to do so.
Also, several colleges and universities and/or faculty thereof, submitted metadata describing sizeable and/or special collections:
IN
Penn State
reports of northwest PA
Relatively large datasets were described by the following private individuals and industry:
Tom Proch—Unionoids of PA
Steven Johnson—Lepidoptera of PA
Collins Pine Co.—landscape ecology
Forest Land Consulting—“big trees” inventory
Sherwin
Family Enterprises—plants and fungi of the
Several non-identified PA biodiversity database holders, who are also non-Pennsylvania groups, have submitted metadata forms for taxa found in PA. These include:
Delaware Museum of Natural History,
Field Museum Department of
Entomology,
Ohio State University Department of
Entomology,
National Park Service—vascular
plants along the
27,000 records of plants collected in PA by Muhlenberg et al from 1740-1820
Forty-one “no metadata to report” forms have been submitted
as of
The Concurrent Session on Biodiversity Information at the
2001 Annual Conference of PBP overwhelmingly requested that the metadata forms
be sorted by County. The participants
recognized that this is not the scientific way to sort, but that it is the
practical way to do so. Since PA’s lands
are governed by entities not necessarily coinciding with ecological boundaries,
they thought that the information broken down by County would be the most
useful to PBP in developing its biodiversity conservation plan. Consequently, the first report, “
I also sorted metadata forms by ID number and also included the ID number, for easy reference to the forms, on all of the reports. I generated a variety of other reports trying to anticipate the interest of the reviewer of the metadata forms. These include metadata forms sorted by:
Taxon
Taxon, More Specific Taxon, and Keywords
Title
Ecological Study (aquatic and/or terrestrial) and Taxon
Physiographic Province
Contact Organization
Can Share Metadata (Yes or No)
The “No Metadata to Report” forms were sorted by ID number and also by organization.
All of these reports are included as Appendices and as MS word rich-text-format-files.
In addition to sorting the data by the various parameters mentioned above, I also analyzed it based on number and types of groups reporting; number of web accessible reports; number and percent of information entirely in electronic format, partially in electronic format, and not in electronic format; number of ecological versus specimen-based reports; number of reports not GIS/GPS referenced, partially referenced or referenced by interpretation, or not GIS/GPS referenced; and by historical and other significance.
Analysis by Organizational Group Reporting and Web-Accessibility:
Table 1 lists the number of reports submitted by type of group. Information about the state’s biological resources is held by hundreds of organizations and individuals both inside and outside Pennsylvania. When searching for comprehensive biodiversity information, an interested individual would have to contact a myriad number of groups to access the information that is available. They may or may not be granted access to the information and they may have to pay a fee for their search. The fee may vary, depending on who they are, what they plan to do with the information, and who they contact for the information.
Most of the biodiversity databases in the Commonwealth are not web-accessible by the public.
Table 1—Summary of Survey Responses Listed by Organizational Category.
TYPE OF GROUP |
# Reports of
Submitted Metadata |
No Data To Report |
# Web-Accessible |
State Government Agencies |
6 (+ 106 from 1999 Bacastow report) |
6 |
0 (106 on PASDA site) |
Federal Agencies |
7 (+ 2 from 1999 Bacastow report) |
0 |
0 (2 on PASDA site) |
Museums & Arboreta |
12 |
0 |
6 |
Colleges & Universities and Field Stations |
58** |
18 |
0 |
Nature Organizations |
11 |
12 |
3 |
Private Individuals & Industry |
10 |
2 |
0 |
PNDI* |
3 (+ 1 from 1999 Bacastow report) |
0 |
3* (+ 1 on PASDA site) |
Townships |
3 |
2 |
0 |
PA Databases outside of PA |
8 |
0 |
5 |
**
Pennsylvania Natural Diversity Inventory (PNDI) is a cooperative partnership of
the Department of Conservation and Natural Resources’ Bureau of Forestry, The
Nature Conservancy, and the Western Pennsylvania Conservancy, and, thus, is not
listed under State Government Agency or Nature Organization. It has a website which is accessible by the
public of a list of plant communities, plant and animal species of special
concern, and rarity ranking definitions at URL
http://www.dcnr.state.pa.us/forestry/pndi/pndiweb.htm
**
PASDA web site: URL http://www.pasda.psu.edu
**40 of the 58 reports were submitted by one field station.
Description of Metadata by format:
Of the 118 metadata reports, 58 describe their data as being entirely in electronic format and 44 as being partially converted into electronic files. Only six are not electronic. Eight reports did not indicate whether the records were in paper or electronic format. All eight of these reported 100% preserved specimens, so I assume they misunderstood the question. I was unable to determine if any of the data was also in another format. I also assume that we received a disproportionate number of electronic or partially electronic databases. I assume that those comfortable with responding to an email query and submitting an electronic metadata report are probably more likely to have begun the conversion of their field notes from paper to electronic format. Those who are uncomfortable with electronic submission, probably would not have filled out a metadata report, and might also be more likely to have paper databases.
All of the Bacastow, et al data has been converted to metadata in an electronic format. It is available on the PASDA web site. However, not all of the databases included in the Bacastow report are entirely in electronic format.
Sixty-nine (58 %) of the PBP metadata reports are not GIS/GPS referenced; 29 (25%) are partially GIS/GPS referenced or are GIS/GPS referenced by interpretation, and 20 (17%) are completely GIS/GPS referenced.
PASDA has GIS/GPS referenced by interpretation those Bacastow et al reports that were not GIS/GPS referenced.
Description of Metadata by taxon:
Only 21 of the PBP metadata reports are strictly specimen-based and not ecological. All of the rest, including most of the large database holders, claim an ecological component even though many are also specimen-based. Of the 97 listed as ecological studies, 33 are aquatic, 39 terrestrial, and 25 both aquatic and terrestrial. Also, several of the ecological databases listed in the Bacastow et al report appear to be primarily species lists and are categorized in Table 3.
Table 2—Taxa Included in the PBP Metadata Survey Reports and the Number
of Species, Records, and Reports.
Taxon
|
Keyword |
Specific Group |
Minimum #
species* |
**#
of records |
*** # of reports |
Bacteria |
All |
|
? |
53 |
1 |
Fungi |
Fungi
|
general |
? |
500+ |
2 |
|
Fungi
|
lichens |
20 |
30 |
1 |
Invertebrates |
All |
|
? |
? |
1 |
|
Special
concern |
|
226 |
1746 |
2 |
|
Crustaceans
|
amphipods |
1 |
? |
1 |
|
|
crayfish |
8 |
900 |
2 |
|
Flatworms
|
planaria |
1 |
? |
1 |
|
|
trematodes |
? |
<200 |
2 |
|
|
cestodes |
? |
<200 |
1 |
|
Insects
|
general |
100 |
1050+ |
6 |
|
|
coleoptera |
70 |
3995 |
2 |
|
|
hymenoptera |
3100 |
130,000 |
1 |
|
|
lepidoptera |
800-1000 |
5100 |
1 |
|
|
plecoptera |
134 |
5600 |
2 |
|
|
tricoptera |
320 |
6000 |
1 |
|
|
macroinvertebrates |
141 |
555+ |
5 |
|
Mollusks
|
|
128 |
320 |
1 |
|
|
unionids |
67 |
2500 |
1 |
|
Nematodes
|
|
? |
<200 |
1 |
|
Plankton
|
general |
? |
? |
1 |
|
|
Leptodora kindtii |
1 |
48 |
1 |
|
Spiders
|
|
104 |
104 |
1 |
Phytoplankton |
|
Chlorophyceae |
? |
168 |
2 |
|
|
diatoms |
? |
144 |
1 |
Plants: Non-Vascular |
Bryophytes |
|
41 |
570 |
3 |
Plants: Vascular |
All |
|
4000 |
670,276+ |
16 |
|
Special
concern |
|
706 |
13,420 |
2 |
|
Ferns
& fern allies |
|
? |
22+ |
2 |
|
Hydrophytes |
all |
? |
173 |
3 |
|
|
bog
plants |
? |
193 |
1 |
|
|
Myriophyllum
excellabens |
1 |
8 |
1 |
|
|
Lemna |
1 |
4 |
1 |
|
Flowering
Plants |
Asteraceae |
2 |
72 |
1 |
|
|
Cactaceae
Opuntia |
1 |
20 |
1 |
|
|
herbaceous
plants |
? |
424 |
2 |
|
|
Juglandaceae |
? |
? |
1 |
|
|
trees |
50 |
72 |
2 |
Vertebrates |
All |
|
100 |
2800 |
1 |
|
Terrestrial
vertebrates |
|
? |
732 |
1 |
|
Special
concern |
|
160 |
986 |
1 |
|
Birds
|
all |
315 |
564,427+ |
14 |
|
|
barred-owl |
1 |
500 |
1 |
|
|
eastern
Red-winged blackbird |
1 |
187 |
1 |
|
|
great
blue heron |
1 |
100 |
1 |
|
|
ovenbird
nesting |
1 |
? |
1 |
|
|
raptors |
7 |
100 |
1 |
|
|
ruffed
grouse |
1 |
80 |
1 |
|
|
tern |
1 |
26 |
1 |
|
|
woodcock |
1 |
70 |
1 |
|
Fishes
|
all |
150 |
7487+ |
5 |
|
|
carp |
1 |
3 |
1 |
|
|
darters |
4 |
44 |
1 |
|
|
mottled
sculpin |
1 |
141 |
1 |
|
|
rosy-faced
shiner |
1 |
57 |
1 |
|
Herps |
all
amphibians & reptiles |
90 |
32,490+ |
5 |
|
|
snapping
turtle |
1 |
67 |
1 |
|
|
timber
rattler |
1 |
70+ |
2 |
|
Mammals
|
all |
100+ |
28,301 |
5 |
|
|
white-footed
mouse |
1 |
5843 |
2 |
* the number listed is the minimum number of possible species reported in the metadata reports
of the taxonomic group listed. (For example, 3 reports on vascular plants listed 706, 3180, and 4000 species recorded in their data; thus 4000 species of vascular plants is the minimum number of species that were reported in this survey.) A “?” denotes that the reporter did not include this information. A “+” is used if the reporter indicated that there were more species than the number indicated.
** the number listed is the total number of records from all the pertinent metadata reports for the
specific group listed. A “+” is used when one or more reports did not indicate the number of records.
*** the reports total more than 118 because some of the reports included information on more than one taxon.
Table 3—Description of Bacastow, et al, Data Relative to
Reporting Agencies, Subject Matter of Report, and Number of Reports Included.
|
Number of Metadata Reports Submitted by Agency* |
|||||
SUBJECT MATTER OF REPORT |
DCNR |
DCNR-Bureau of
Parks |
DCNR-Bureau of
Forestry |
PGC |
PFBC |
Misc. ** |
Other*** |
6 |
2 |
4 |
6 |
18 |
4 |
Ecological |
3 |
2 |
4 |
2 |
10 |
3 |
Plants |
|
|
3 |
|
|
1 |
Trees/Timber |
|
|
5 |
1 |
|
|
Insects & Disease |
|
|
1 |
|
|
|
Birds |
|
|
|
4 |
|
2 |
Eagle |
|
|
|
1 |
|
|
Grouse/woodcock |
|
|
|
2 |
|
|
Mourning
dove |
|
|
|
1 |
|
|
Waterfowl |
|
|
|
5 |
|
|
Special
Concern |
|
|
|
1 |
|
|
Mammals |
|
|
|
2 |
|
|
Bat |
|
|
|
3 |
|
|
Bear |
|
|
|
1 |
|
|
Deer |
|
1 |
|
4 |
|
|
Woodrat |
|
|
|
1 |
|
|
Winter Mortality |
|
|
|
1 |
|
|
Road Kill |
|
|
|
1 |
|
|
Fish & Wildlife |
|
|
|
1 |
|
|
Fish |
|
|
|
|
6 |
|
Macroinvertebrates |
|
|
|
|
4 |
|
Mussels |
|
|
|
|
1 |
|
* the total number of reports is greater than the 109 included in Bacastow, et al, because some agencies share the same dataset. For example, the scientific collectors database is shared by DCNR, PFBC, and PGC. This information is entered three times, once each for each agency, under the subject category of “Other.”
** several Bacastow, et al, reports indicated no author/owner or an author/owner other than DCNR, PFBC, or PGC (for example, PENNDOT and the US Forest Service reports were submitted.) These are listed under “Misc” in the number of reports submitted by agency.
*** many of the reports included under the subject category “Other” are datasets on boundaries, violators, recreational users, permits, etc.
Description
of Metadata by Historical and other Significance:
Two collections date back to the 1700’s. The National Academy of Science has a lichen type collection of 20 species collected from 1780-1815. The Liverpool Museum has 27,000 records of plants collected in Pennsylvania by Henry Muhlenberg and John Bartram between 1740 and 1820. The Morris Arboretum Pennsylvania Flora Database has plant records pre-1800 through the present and has 3180 species and 450,000 specimens.
Several collections date back to the 1800’s:
Plants:
Ferns and allies: 1800—200 records at the Academy of Natural
Sciences
Vascular plants: 1800—4000 species and 148,000 records at the
Carnegie Museum of Natural
History
1800—706 species and 9783 records of species
of special concern at
Pennsylvania Natural
Diversity Inventory
1880—22,000 records at Wayne E. Manning
Herbarium at Bucknell University
Vertebrates:
Birds: 1820—8000
study skins at Academy of Natural Sciences
1845—315 species and 18,861 records at
Carnegie Museum
Amphibians & Reptiles:
1885—90 species and 27,411 records at
Carnegie Museum
Fishes: 1894—150
species and 7463 records at Academy of Natural Sciences
Mammals: 1898—76 species and
25,234 records at Carnegie Museum
All Vertebrates 1850—160 species and 1986 records of
special concern species at PNDI
1860—732 PA species at Museum of Vertebrae
Zoology, University of
California, Berkeley, CA
Invertebrates:
Staphylinidae of Order Coleoptera:
1887—20 species and 897 records at Field
Museum of Natural History,
Chicago, IL
Mollusks: 1890—128 PA
species and 320 records at Delaware Museum of Natural
History
All Invertebrates: 1850—226 species and 1746 records of special
concern species at PNDI
Appendices (file names):
Metadata Sorted by County
Metadata Sorted by ID#
Metadata Sorted by Title
Metadata Sorted by Taxon and Keywords
Metadata Sorted by Taxon
Metadata Sorted by Physiographic Province
Metadata Sorted by Ecological Study_Taxon
Metadata Sorted by Contact Organization
Metadata Sorted by Can Share
NoMetadata by report ID
NoMetadata Sorted by Organization
Metadata List
Additional Material:
Data provided by Thomas Ford, PFBC
Hard copy of materials included in Bacastow, et al, report of 1999.
Electronic version of material in Bacastow, et al, report of 1999.
Electronic copy of website of metadata form,URL
http://www.upb.pitt.edu/ainh/metadata/index.htm
Electronic copy of website of metadata reports, URL
http://www.upb.pitt.edu/ainh/metadata/dataview.asp
Electronic copy of website of no metadata to report, URL
http://www.upb.pitt.edu/ainh/metadata/nometadatareport.asp
Electronic copy of mailing list