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Natural History Museum of the Sabah Parks

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Biological Collection Management in Sabah, Malaysia - How Do We Share Data?

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Natural History Museum of the Sabah Parks

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Interpretation, dissemination and sharing of museum's collections information have always been among the main

roles and functions of any museums worldwide. The main purpose is to safeguard our precious, priceless and

irreplaceable cultural, historical and natural heritage. However, despite the transparent nature of museums, the 1987

International Councils of Museums (ICOM) Statutes, “Code of Professional Ethics, the UNESCO's Conventions on

"The Guarding of Cultural Property” Conventions of 1977, and the Sabah Museum's "Collection Policy and

Procedures" of 2000, stipulate vividly that data sharing in museums, including natural history collections that contains

a significant amount of highly sensitive items, should be, handled with utmost care and ethically scrutinized based on

current local and international laws, conventions and aspirations. It is therefore prudent to say that access to

collections' data or data sharing should be based on a sound bilateral retribution on the code and ethics of museums

collections management. While the Sabah Museum in principle accepts the possibility of data sharing in an

equitable and smart manner it should be deemed appropriate that bona fide accomplices involved should strictly

adhere to the current local and international laws, conventions and aspirations. The contention is intended to tacitly

instruct and bind all concerned to the highest ethical practices and standards of museology not just for the sake of

sharing and accessing data. The modus operandi of data sharing could be spelled out in various approaches, via the

Information and Communication Technology (ICT) or preferably through the physical access to the primary records at

the repository premises. As rule of the thumb, only general optimal information that sufficed for the BBEC program

should be entered in any electronic ICT systems. Further sensitive information need to be quired from the primary

source.

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1.6 Administering Data: The Museological Wayby Datuk Joseph Pounis Guntavid & Mr. Jaffit Majuakim, Sabah Museum

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Administering Data: the Museological Way

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Linking Up With ITBC Data Management Unit: A Proposal

Institute for Tropical Biology and Conservation (ITBC) Universiti Malaysia Sabah (UMS) was formed with the main aim

of becoming a centre of excellence for research and learning/teaching of tropical biology and conservation of the

terrestrial and freshwater ecosystems. The institute then identified four thrust areas: Biosystematic and Biodiversity;

Ecological Processes; Advancement of Biodiversity and Nature Tourism.

To facilitate implementation of its plan of operation in line with the four thrust areas of research and teaching/learning,

four divisions were formed: Administration and Finance (A&F); Research and Development (R&D); Reference

Collection Centre (BORNEENSIS) and Information Network (IN). Although, these four divisions have clear roles and

functions, there is a certain amount of over lapping and interdependency, which ensure integrity among the staff and

stakeholders.

In this paper the roles and functions of BORNEENSIS is being presented.

BORNEENSIS

ITBC allocated Biosystematics and Biodiversity as the most important thrust area. To ensure efficiency in doing both

research and teaching/learning of the thrust area, which will lead to increased awareness and effort to conserve

biodiversity and ecosystem among the stakeholders, one of the most important aspect is inventoring species in the

Borneon terrestrial and freshwater ecosystems, including their uses. Thus, a central facility is created, called

BORNEENSIS. This facility is a repository for both specimens (dead and alive) and data (including traditional knowl-

edge on uses of biodiversity).

Physically BORNEENSIS comprises of storage facilities for dead reference specimens and they are four

collection rooms (The Insect Collection, Wet Collection, Dry Collection and Herbarium). Living materials are reared

and maintained in one of the four outdoor facilities (Insect House, Green house, Animal House and Ex-situ Conser-

vation Valley). Information are kept several ways - in written forms (theses, dissertation, reports, books) or as slides,

photograph and CDs. All these are kept in the Resource Room.

To maintain a good and useful reference collection, a data management system has to be efficient. More than 50% of

the global biodiversity of 1.75 million species lies in the tropical rainforest (a total of 7% world surface area). And

scientist such as Wilson and Erwin estimated there are about 5 to 30 million species of livings things. Thus, we

reckon there will be substantial amount of data to be dealt with at ITBC in the near future. These data will be logged

into computer and should be easily accessed by stakeholders, within and from outside Malaysia.

1.7 Linking Up With ITBC Database Management Unit: A Proposalby Prof. Datin Dr. Maryati Mohamed, Institute for Tropical Biology & Conservation, UMS

Linking Up With ITBC Database Management Unit: A Proposal

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ITBC Database Management Unit (DBMU)

Opportunity to acquire on effective and efficient database management system came to ITBC under the Bornean

Biodiversity and Ecosystems Conservation (BBEC) programme. Realizing the need to develop BORNEENSIS, ITBC

requested for a JICA technical cooperation assistance in 2001. The request was granted in 2002 and the technical

cooperation was expanded to also cater for the state needs. This assistance was then called BBEC programme.

Not losing sight of ITBC initial request to develop BORNEENSIS, JICA will provide a database management system

to ITBC. It is hoped that this will be a model set up for the region. The system is envisioned to be realized by first

quarter of JKY 2003/04.

Training will be carried out and test runs made using specimen already available and those collected recently. By end

of third quarter of JFY 2003/04 ie September the database management system should be fully operational. The data

then can be retrieve by stakeholders, within Sabah such as Forestry Department, Sabah Park and Sabah Museum

and other schools in UMS.

The next step would be to link up with other existing database management systems within Malaysia. Some possible

linkages can be made with Universiti Kebangsaan Malaysia, Universiti Malaya and NIASTIC.

Eventually ITBC DBMU will link up with international database system. At present ITBC is aware of ECOPORT (based

in Australia), species 2000 (Reading University, UK) Systematic Agenda International (American Natural History

Museum, NY), Global Taxonomic Initiative (Montreal, Canada) and Global Biodiversity Information Faculty (GBIF,

Netherlands).

Data kept will be tailor made to ITBC needs as well as taking into account the global needs. Images of specimens

and sound library will be available in the long term.

Partnership and Linking Up

ITBC is fully aware that the Sabah Biodiversity Enactment will be operational soon and will be considered as the

ultimate governing ruling with regard to access to genetic resources in Sabah. Nontheless, as the Enactment was

formulated to facilitate access to and benefit sharing of the use of biodiversity, and ITBC consider acquiring and

keeping data as a prerequisite to other efforts leading to use of genetic resources, ITBC activities will not be

contravening the enactment.

DBMU at ITBC is prepared to assist Sabah Biodiversity Centre (SBC) by becoming one of its node where data can be

accessed freely through a networking. This link and partnership will benefit both UMS and SBC. ITBC, UMS has

committed itself to be a repository centre for specimen and data of Borneo. SBC could use the data to complement its

own database.

Similarly Sabah Park and Sabah Museum can network with DBMU at ITBC. They need not spend time collecting,

curating and maintaining specimen and information. Their resources can be useful elsewhere.

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Part 2

PCM Workshop:How to Establish Network

for Data Sharing?

2.1 PCM Workshop - How to Establish Network for Data Sharing?The Project Cycle Management (PCM) Workshop

Moderator:

Dr. Mohd. Nazri Iguchi Abdullah (JICA)

Participants:

1. Iman Ali

2. Ag. Binting Drainage and Irrigation Department

3. Lina Mohamad Lin Science and Technology Unit

4. Fatimah Jaafar Science and Technology Unit

5. Rimi Repin Sabah Parks

6. Rose John Kidi Innoprise Sdn. Bhd.

7. Dr. Homathevi Rahman Universiti Malaysia Sabah

8. Dr. Isabelle Lackman-Ancrenaz HUTAN

9. Azman Mohammed Universiti Malaysia Sabah

10. Tn. Hj. Amat Ramsa Yaman Rainforest Academy, Universiti Putra Malaysia

11. Nurhuda Manshoor Universiti Malaysia Sabah

12. Kelvin B.H. Kueh Universiti Malaysia Sabah

13. Dr. Monica Suleiman Universiti Malaysia Sabah

14. Dr. Chey Vun Khen Forest Research Centre

15. Wendy Wan Economic Planning Unit, Sabah

16. Dr. Jamili Nais Sabah Parks

17. Maklarin Lakim Sabah Parks

18. Kenneth Sion Sabah Parks

19. Fatimah Simin Sabah Parks

20. Faizal Ahmad Environmental Conservation Department

21. Sabrina Salimi Environmental Conservation Department

22. Raymond Alfred AREAS; WWF Malaysia

23. Dr. Arthur Chung Forest Research Centre

24. Dr. Menno Shilthuizen Universiti Malaysia Sabah

25. Jaffit Majuakim Sabah Museum

26. Azmi Salim Ranau District Office

27. Joseph Bangguan Tuaran District Office

28. Dr. Junko Shimura Global Taxonomy Initiative

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Participants:

29. Assoc. Prof. Dr. Yoshiaki Hashimoto JICA Expert - Universiti Malaysia Sabah

30. Bakhtiar Effendi Yahya Universiti Malaysia Sabah

31. Hairul Hafiz Mohamad Universiti Malaysia Sabah

32. Jimmy Omar Sabah Nature Club

33. Dr. Takuji Tachi JICA Expert - Universiti Malaysia Sabah

34. Allen Chia Sabah Tourism Board

35. Nell Baker Global Canopy Program

36. Dr. Stephen Sutton Borneo Books

37. Prof. Datin Dr. Maryati Mohamed Universiti Malaysia Sabah

38. Minar Yugat Ministry of Tourism, Environment, Science and Technology

39. Moktar Yassin Ajam Science and Technology Unit

40. Hiew Nget Yin IT Development Unit

41. Melvin Gumal Wildlife Conservation Society - Malaysia Programme

42. Dr. Edwin Bosi SOS Rhino

43. Takashi Fueda Fujitsu Malaysia

44. Shigeo Sakai JICA Expert - Sabah Parks

In the workshop at first, the participants agreed that their common objective is to “Establish an effective electronic

networking for sharing of biodiversity database among institutions with a possibility for expansion to other parts of

Malaysia and internationally. Then, the participants dicussed means and conditions to achieve the common

objective. The participants wrote their ideas on cards and paste them on the wall for open discussion. The cards were

then placed into “tree” shape by the participants as shown below in the attached diagramme. This is called an

“Objective Tree” which represent “mean-ends” relationship between the cards. In other words it shows the way to

achieve the common objective.

PCM Workshop - How to Establish Network for Data Sharing?

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Mr. T. Kusano, Chief Advisor for BBEC thanked everyone for their participation in the PCM workshop. He was most

happy to note everybody’s interest to contribute.

To make biodiversity information integrated for BBEC, we need to establish a network for data sharing. Therefore, all

suggestions given are very valuable. There is no centrepoint approach here, as each centre is equally important, and

new technology make all these ideas possible. The important strategy is to make applications for database

management uniform, and this can be established with helpful suggestions, as was done in this workshop. I hope

to have more workshops in future, and that the Institute for Tropical Biology and Conservation can be used as a model

to build such an application and support the establishment of collection management database at the other research

institutions in Sabah and networking them.

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Part 3

Collection data and theirmanagement in Sabah

IntroductionTo conserve biodiversity in a region, we have to know how many and what kinds of species are found here. Suchinformation is only obtained from specimens collected by our inventory efforts. Thus, establishment of specimen

collection representative of the region’s biodiversity is an important goal for inventory. However, the data associatedwith specimen, rather than the specimens themselves, can be used directly for understanding of biodiversity.Therefore, management of the collection data is just as important as the collection of specimens. The data

management, if carried out properly, can avoid loss information, increase the accuracy of translating data from fieldto analysis, and save many hours of frustration and wasted time.

Necessary steps for the data management are 1) Data recording, 2) Data computerization, 3) Data storage andhandling 4) Data summarizing, 5) Data dissemination, and 6) Data sharing. This chapter outlines these steps, andpresents guidelines and tools required for appropriate collection data management (Fig. 3.1-1).

Collection Data Management3.1 Yoshiaki HASHIMOTO

(Quoted from Chapter 4 in “Inventory & Collection” (2002) UMS/BBEC publishing)

Fig. 3.1-1 Necessary steps and tools required for appropriate collection data managementSP: Spreadsheets Procedures, CMD: Collection Management Database

Specimen based

Species based

Data recording

Data computerization

Data storage and handling

Data summarizing

Data dissemination

Data sharing

Conservation

Action

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SP

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CMD

CMD

GIS

LabelLogbook

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NetworktoolsHigh

Low

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a U

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Collecting CurationHousingPreparation Identification

Specimen Curation step

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Data recordingThe specimen data consist of 1) specimen categories (whole individual, skin, tissue, photo, voice, etc.), 2) collection

sites (latitude and longitude, place name, country name, etc.), 3) collector’s name, 4) collection dates, 5) collectingmethods, 6) mounted state (pinned, fluid-preserved, slide-mounted, etc), 7) specimen type (holotype, paratype,reference collection, etc.), 8) storage locations (Herbarium, Gene bank, etc.), 9) common and scientific name, 10)

physical condition (sex, developmental stage, etc.), 11) ecological and habitat information (primary forest, secondaryforest, distributed area, etc.), and 12) multimedia data (images, video, audio, etc). These data items show propertyof each specimen, and are related to each other. Thus, the data items of each specimen should be recorded in a

manner to enable one to trace all the linkage.

One recommended way of data recording is to give a unique ID number (field number, collector number, registration

number, etc.) to each specimen. And then, into labels, logbooks and computers, all data items of each specimenare recorded as a dataset linking with the ID number.

The data items of specimens must not be recorded as discrete datasets pertaining to taxon names (i.e., family,genus or species names). For example, all specimen data will be recorded separately in each species name. Ifspecies name attached to a specimen changes, the dataset linked to the species name losses its usefulness. In

fact, taxon names can never be completely stable. They often change because of new data, new interpretations ofexisting data, difference of opinion, misidentification names, etc. And then, single species is split between two ormore species or two species are grouped together into singe species. It is important to remember that the taxon

name is only one item of specimen data.

Data computerizationThe data computerized can be easily transmitted, and integrated with advanced means of analysis. Accordingly thecomputerization is a necessary step to collection data management.

Word processors and spreadsheet procedures are available to computerize the data. However, word processorsare not the best choice for data computerization. Word processors are designed to make line of words, so that theirfunction for data entry is very poor. And, they are extremely limited in transferring data files into other different data

formats or software. Spreadsheet procedures, such as Microsoft Excel, may be the most effective approach oftransferring specimen data into computer files. Spreadsheets record data in tables of labeled columns and rows.Titles of data item (i.e. locations, dates, specimen-type) can be placed in the columns and rows. Many timesaving

data entry tools, such as auto-numbering, are included in the program. Finally, The data can be exported in manydifferent formats. Excel is easy to use for everybody, in portable computers, and on both Windows and Mac OSplatforms. These points make it ideal software for data computerization.

However, the data stored in tables are cumbersome to add new data and re-format into them. And, these worksusually are time consuming for inventory’s results, because inventory generates extensive collection data. Thus,

this way should be used only as data entry, and then the data should be transferred to more sophisticated datamanagement systems, such as relational database. In this point, an important aspect of data-computerization is toconsider the format of allowing easy data transfer from sheet to the database system. Matching of data format

between Excel worksheet and database should be established in the planning of collection data management. Ifyou have no database system at present, you are usually better off using the following format: Within Excel worksheeta row is created for each specimen. ID number of each specimen is entered in Column 1, and then each data item

is recorded within separate columns (Fig. 3.1-2). For example, scientific names are entered in genus name columnand species name column separately. Collection localities are also entered within separate columns (e.g. place1,place2, state or province, country). Excel can fuse data-cells automatically, but, if data contained in a cell is separated,

it requires you many hours of frustrating work. Thus, this way will save wasted time of data reformatting to transferdata from worksheets to database.

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Fig. 3.1-2. A sample of worksheet

Another important aspect for the step is to proof data. If specimen data was entered into a computer file, then thedata must be checked for any keystroke errors introduced during data entry. Printed hard copy is one way to catching

data-errors. Using a dual entry procedure is another way to data checking. Two different operators enter the samedata into different files. Any mismatches between the two are noted, and the original data are checked to determinewhich file is in error.

Data storage and handlingRelational databases are ideal tools to store and handle collection data. In relational database, the stored data are

linked to each other by ID-number (Fig. 3.1-3). When new data or items are added to relational database, suchchanges are automatically applied and linked to all relevant data through ID-number, without changing datasetformat. The feature of relational databases is most suitable to manage large amounts of specimen-based data.

There is a variety of relational database-software. Personal software of relational database, such as MicrosoftAccess and File Maker, may be used for the collection data management. However, these programs are designed

for general use, and they need intensive customizations in several ways to fulfill functions for the purpose. Specializeddatabase software for collection management (Collection management database), like Musetheque, Biota andPlatypus, is recommendable. Collection management databases are designed as specific tools to store and

handle collection data, and they are particularly good in 1) rapid checking of specimen data, 2) well data preservation,and 3) well data security, as follow:

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1) Rapid checking of specimen dataAs the quantity of database becomes large, it becomes difficult to find a dataset associated with a particular

specimen from database. Even if ID-code tags are attached to each specimen, long code entry may introducekeystroke errors. Most collection management databases are equipped with barcode system as way to retrievedata from specimen directly. By using of barcode-reader and barcode attached to each specimen, the data

corresponding to any specimen can be accessed rapidly and checked accurately.

2) Well data preservation

Hardware and software crash, and also user failures, occur on an unpredictable schedule. Thus, a backup of thedatabase should be made periodically, especially for great deal of data. However, it is usually difficult to maintainregular backup schedule. Most collection management databases facilitate data preservation and recover functions.

In the functions, deleted data is automatically preserved into external computer files, so that data loss is preventedand current data can be replaced with previous data when needed.

3) Well data securitySecret information, such as rare species distribution, usually is included in inventory results and the informationshould be protected from outsiders. Most collection management databases can set access permission to each

operation (e.g. data input and out, viewing and printing) for each user type. Such function allows viewing specificdata to only selected type of users. It is good to protect inventory data from outsiders.

Data summarizingCollection data of inventory should be summarized in checklists and catalogue to make it available for biodiversitystudies and conservation planning. In checklists, collection data will be summarized in a taxonomically arranged

report, which includes at least 1) taxon name (order, family, tribe, species etc.), 2) author name of the taxon, and 3)distribution data (province, district, range of elevation, site description, etc.). In collection catalogue, they aresummarized in a list, including at least 1) registration number, 2) type of specimen, 3) taxonomic information

(species names etc.), 4) collecting data (collector, locality, date), and 5) physical condition (sex, developmentalstage, etc.). Preparing such products require sifting numerous collections, refining data, and then formatting thefinal outputs for publication. Those are extremely time consuming works. And more, careful works are required to

avoid cross-contamination of data and misspelling of names.

By using word processors and spreadsheet procedures, the data summary may be generated. The data are

entered and sorted by spreadsheet software at first step and then exported into word processor for editing andformatting. However, this may be cumbersome work. When you find some mistakes in final output files, you shouldcheck original spreadsheet files and occasionally repeat the routine work from the first step. If the data were stored

in collection management database, a few keystrokes can generate checklists and catalogue. Most collectionmanagement databases are equipped with sorting, editing and report creating functions, so that the products canbe automatically generated from the data stored. In addition, some of them have Dictionary reference function,

which register terms and names in dictionary files and check spelling of data with the files. The function can helpyou to avoid misspelling of names and to ensure the integrity of your products. Thus, collection managementdatabases are also recommendable as report producer.

Collection data can also be summarized in distribution maps of species, vegetation, and ecosystems. These mapsare effective to display and understand biodiversity in a region. To generate distribution map, GIS (geographic

information system) based software, like ArcView, is useful. The software offers powerful data mapping andmultimedia display. Some GIS software packages have modes to enter and store collection data. However, this isway of data recording in taxon-base, such as species name. And, The data may not be easily transferred from one

GIS software package to another. Because most of the software packages readily import data from collectionmanagement database, it is better to use GIS software only for data mapping.


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Fig. 3.1-3. Collection management database system

Species B

Locality A

Species A

Locality B

Collecting Data A Species ASpecimen 3

Locality A

Collecting Data B

Specimens and the data

Specimen 1

Specimen 1

Specimen 2

Specimen 2

Specimen 3

Specimens Worksheet

Collecting Data C

Collecting Data C Locality A Species B

Locality B

Locality A

Species A

Species A

Collecting Data A

Collecting Data B

ID No. 1

ID No. 2

Specimen 1

Specimen 2

Specimen 3

ID No. 3

Species A

Species A

Species B

Locality A

Locality B

Locality A

Species Check List

Collecting Data B

Collecting Data A

Collecting Data C

ID No. 1

ID No. 3

Data access

Specimen management

Collection management database

Report writing

Collecting Data B

Collecting Data C

Collecting Data A ID No. 1

ID No. 2

ID No. 2

ID No. 3

Locality A

Locality B

Species A

Species B

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Data disseminationYour inventory’s results should be disseminated not only to your collaborators, but also to worldwide communities

of scientist, politician and industry, as well as to the general public. Such dissemination is useful to appealimportance of your biodiversity inventory and increase your supporters.

Internet is the most effective means to deliver information to worldwide communities. Thus, you should try topublish the summary of collection data by Web pages on Internet. A good example of Web publication for collectiondata is showed in Web site of INBio (Institute National Biodiversity, Costa Rica) (http://darnis.inbio.ac.cr/ubis/). The

Web publication includes a photo and a distribution map of the species in Costa Rica, which is generated from theinformation contained in “Atta”, collection management database of INBio.

Simple reports may be published on Web by only using personal Web-publishing software. However, such publicationof INBio Web-site requires expert knowledge of Internet technology. Fortunately, because computer technology hasadvanced, some modern packages of collection management database have Web-based data exploration system.

In the system, Web pages about data summary or Web-based database are generated automatically from collectiondata stored (Web-based database is a search tool that allows users to access databases through the Web-site).If you want to establish the Web-site like INBio, introduction of such collection management database may be the

most efficient way.

Data sharingFinally, consideration for data sharing is also important to make inventory’s results really available for conservationof biodiversity. There are so many groups of organisms in most habitats. And, there are limitations in facilities,equipment and other resources, man-power and specialist expertise. It is therefore obvious that rapid way to

understand biodiversity is exchanging and sharing existing inventory results. In fact, many regional and internationalefforts are underway to establish network for linking biodiversity information across multiple databases, i.e. TaxonomicDatabase Working Group, Global Biodiversity Informatics Facility (GBIF), Global Taxonomic Initiative (GTI) etc. You

should try to establish such network, or link your database with the network.

For exchanging of data, the database system having flexibility in data import and export is useful. Check carefully

what type of files can be exported and imported by the database, in planning the database introduction. Somenetwork established “flat file” structure for transferring data across multiple databases. It is also better to checksuch file structures before entering large datasets into your database.

ConclusionsThree major conclusions emerge from this overview:

1) The necessary protocol at inventory data management is keeping the information associated with each specimenand making it available. Thus, the data should be recorded in specimen base structure, not in taxon base structure.

2) Inventory work generates extensive collection data. Thus, to manage the data, sophisticated tools are needed(see Box 1). The specialized relational database for collection management is especially recommendable. The

database is useful to store, handle, summarize, and disseminate the collection data.

3) Data sharing among collaborators is an effective way to make results of your inventory available for biodiversity

conservation. Check carefully to make sure that the data can be easily linked across multiple databases.


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Box 1. Summary of Computer Software Program for Collection Data management

1.Word processorsRecommended Uses: Printing of data label of specimen

2.Spreadsheets ProceduresRecommended Uses: Data Computerization

3.Collection management databaseRecommended Uses: Data storage, handling, summarizing and dissemination

4.GIS based softwareRecommended Uses: Data mapping and display

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Documents

Slide 1 Slide 2 - Sabah 25-48.pdf · Slide 1 Slide 2 Slide 5 Slide 6 ... Slide 1 Slide 2 Slide 5 Slide 6 Slides Presentation ... 42. Dr. Edwin Bosi SOS Rhino 43