Flora Sumatra: Digitizing and data basing specimens of the Sumatran Flora deposited at Herbarium Universitas Andalas (ANDA)-Part 2

Latest version published by Herbarium of Andalas University on May 23, 2022 Herbarium of Andalas University

Herbarium of Andalas University (ANDA) is one of the active herbaria in Sumatra, Indonesia. Our herbarium host specimens mainly from Sumatra and adjacent islands, but limited numbers of collections also available from elsewhere. Since its establishment in 1983, the herbarium collections have grown with over 65,000 sheets of specimens. Although the collections are actively being used for research and education by locals and internationals, the lack of a database system has made the collections hard to access. Since 2018, we have worked with the Global Biodiversity Information Facility (GBIF) to catalog and digitize our collections. Here we reviewed our cataloged specimens. Until now, we have cataloged more than 31,000 of sheet specimens from 1700 species in 340 genera and 29 families of vascular plants. Those are reported in several datasets. This dataset elucidated the geo-referenced data from 676 species in 255 genera within 14 families of vascular plants. Among all of the families we have cataloged here are Acanthaceae, Anacardiaceae, Annonaceae, Apocynaceae, Compositae, Convolvulaceae, Cucurbitaceae, Ebenaceae, Lauraceae, Leguminosae, Melastomataceae, Primulaceae, Rutaceae, Ulmaceae. Among them are 3 species that are endemic to Sumatra, Endangered (1 species) , Near Threatened (1 species), Vulnerable (8 species), Least concern (79 species) and 1 species protected under Indonesian government regulation. This data mobilazation program is our first step to improve research and education for plant species in Sumatra.

Data Records

The data in this occurrence resource has been published as a Darwin Core Archive (DwC-A), which is a standardized format for sharing biodiversity data as a set of one or more data tables. The core data table contains 17,600 records.

This IPT archives the data and thus serves as the data repository. The data and resource metadata are available for download in the downloads section. The versions table lists other versions of the resource that have been made publicly available and allows tracking changes made to the resource over time.

Downloads

Download the latest version of this resource data as a Darwin Core Archive (DwC-A) or the resource metadata as EML or RTF:

Data as a DwC-A file download 17,600 records in English (451 KB) - Update frequency: continually
Metadata as an EML file download in English (67 KB)
Metadata as an RTF file download in English (33 KB)

Versions

The table below shows only published versions of the resource that are publicly accessible.

How to cite

Researchers should cite this work as follows:

Nurainas N, Taufiq A, Handika H, Harapan T S, Syamsuardi S (2022): Flora Sumatra: Digitizing and data basing specimens of the Sumatran Flora deposited at Herbarium Universitas Andalas (ANDA)-Part 2. v1.8. Herbarium of Andalas University. Dataset/Occurrence. https://doi.org/10.15468/55evew

Rights

Researchers should respect the following rights statement:

The publisher and rights holder of this work is Herbarium of Andalas University. This work is licensed under a Creative Commons Attribution Non Commercial (CC-BY-NC) 4.0 License.

GBIF Registration

This resource has been registered with GBIF, and assigned the following GBIF UUID: 39e85504-1ebe-4671-be65-19ccdc1d7c7d.  Herbarium of Andalas University publishes this resource, and is itself registered in GBIF as a data publisher endorsed by Indonesian Biodiversity Information Facility.

Keywords

Occurrence; Specimen; Occurrence

Contacts

Who created the resource:

Nurainas Nurainas
Head of Herbarium
Herbarium of Andalas University (ANDA) Limau Manis 25163 Padang West Sumatra ID +6281310818597
Ahmad Taufiq
Data Manager
Herbarium of Andalas University (ANDA) Bandar Buat 25163 Padang West Sumatra ID +6281363457262
Heru Handika
Researcher
Museum of Natural Science and Department Biological Sciences, Louisiana State University Baton Rouge US +12259165691
Try Surya Harapan
Content Provider
Herbarium of Andalas University (ANDA) Palimo Indah Padang West Sumatra ID
Syamsuardi Syamsuardi
Curator
Laboratory of Plant taxonomy, Department of Biology, Mathematics and Natural Science, Andalas University Parak Karakah Padang West Sumatra +6281374777749

Who can answer questions about the resource:

Nurainas Nurainas
Head of Herbarium
Herbarium of Andalas University (ANDA) Limau Manis 25163 Padang West Sumatra ID +6281310818597

Who filled in the metadata:

Ahmad Taufiq
Data Manager
Herbarium of Andalas University (ANDA) Bandar Buat 25163 Padang West Sumatra ID +6281363457262

Who else was associated with the resource:

User
Ahmad Taufiq

Geographic Coverage

The specimens hosted at the Herbarium of Andalas University (ANDA) are primarily from Sumatra. With 473,481 km² in size, the island is the sixth biggest island in the world. It is tropical island located at the coordinate 0° 0′ 0″ N, 102° 0′ 0″ E. The specimens hosted at the herbarium were from several provinces, such as West Sumatra, Jambi, Riau, North Sumatra, Aceh, Bengkulu and Lampung. The specimens were also collected from conservation areas on Sumatra, such as the Kerinci Seblat National Park, Siberut National Park, Lembah Harau Nature Reserve, Rimbo Panti Nature Reserve, Lurah Berangin Nature Reserve, Bung Hatta Forest Park Conservation Area, and Syarif Hasyim Forest Park Conservation Area. All of the collections were collected from wide range of altitudinal elevations and habitats, from lowland tropical forest up to highland forest as well as montane forest on the Bukit Barisan Mountains. In general, the collections were from volcanoes on Sumatra, such as Mt. Sibayak, Mt. Sinabung, Mt. Sorik Merapi, Mt. Pangulubao, Mt. Sibuatan, Mt. Talamau, Mt. Sago, Mt. Marapi, Mt. Singgalang, Mt. Tandikek, Mt. Gadut, Mt. Talang, Mt. Tujuh, Mt. Kerinci, Mt. Pesagi.

Bounding Coordinates South West [-6.141, 94.966], North East [7.711, 108.193]

Taxonomic Coverage

We have digitized 17,600 sheets of specimens in the group of Magnoliopsida. Consisting of 14 families: Acanthaceae, Anacardiaceae, Annonaceae, Apocynaceae, Compositae, Convolvulaceae, Cucurbitaceae, Ebenaceae, Lauraceae, Leguminosae, Melastomataceae, Primulaceae, Rutaceae and Ulmaceae. In total, we have digitized 631 species, 118 in genera rank and 194 in family rank. The most digitized specimens in amount are Leguminosae and Melastomataceae. Among all of the species that have been digitized, 96 species are listed in IUCN Redlist database, consisting of Least Concern (85 species), Data Deficient (3 species), Vulnerable (6 species), Near Threatened (1 species) and Endangered (1 species) (IUCN, 2019).

Family  Acanthaceae (Acanthus),  Anacardiaceae (Mangga-manggaan),  Annonaceae (Custard Apple),  Apocynaceae (Dogbane),  Compositae (Aster),  Convolvulaceae (Binweed),  Cucurbitaceae (Labu-labuan),  Ebenaceae (Kayu Hitam),  Lauraceae (Madang-madangan),  Leguminosae (Polong-polongan),  Melastomataceae (Melastomata),  Primulaceae (Primrose),  Rutaceae (Jeruk-jerukan),  Ulmaceae (Elms)
Genus  Alyxia (Palasan),  Ardisia (Coralberry)
Species  Acanthus ilicifolius (Jeruju),  Andrographis paniculata (Sambiloto),  Asystasia gangetica (Rumput israel),  Graptophyllum pictum (Caricature plant),  Justicia adhatoda (Baja hitam),  Justicia gendarussa (Gandarusa),  Justicia procumbens (Water willow),  Pachystachys lutea (Lolipop),  Sanchezia nobilis (Marathi),  Strobilanthes hamiltoniana (Bunga lonceng cina),  Anacardium occidentale (Jambu monyet),  Bouea oppositifolia (Plum Mango),  Buchanania arborescens (Sparrow's mango),  Campnosperma auriculatum (Tarantang),  Gluta elegans (Rengas),  Mangifera odorata (Kuwini),  Anaxagorea javanica (Akar angin),  Annona muricata (Sirsak),  Annona reticulata (Buah nona),  Cananga odorata (Kenanga),  Meiogyne cylindrocarpa (Indian rosewood),  Monoon fuscum (Mempisang),  Polyalthia cauliflora (Merpisang),  Adenium obesum (Desert rose),  Allamanda cathartica (Allamanda),  Alstonia angustiloba (Pulai Hitam),  Alstonia macrophylla (Pulai),  Alstonia scholaris (Pulai),  Alstonia spatulata (Pulai gabus),  Catharanthus roseus (Tapak dara),  Dyera costulata (Jelutung),  Kopsia fruticosa (Kopsia merah muda),  Nerium oleander (Bunga jepun),  Plumeria rubra (Bunga kamboja),  Tabernaemontana divaricata (Melati mini),  Tabernaemontana pauciflora (Melati hias),  Voacanga foetida (Kalempong gajah),  Acmella paniculata (Jotang),  Adenostemma lavenia (Palau),  Ageratum conyzoides (Siamih),  Anaphalis javanica (Edelweiss jawa),  Anaphalis latifolia (Edelweiss),  Anaphalis longifolia (Anaphalis),  Artemisia vulgaris (Baru cina),  Bidens pilosa (Ketul),  Clibadium surinamense (Conami),  Conyza sumatrensis (Tall fleabane),  Coreopsis grandiflora (Large-flowered tickseed),  Cosmos caudatus (Ulam raja),  Cosmos sulphureus (Sulfur cosmos),  Eclipta prostrata (Urang aring),  Elephantopus tomentosus (Woolly Elephant's Foot),  Erechtites valerianifolia (Tropical burnweed),  Euchiton japonicus (Father-and-child plant),  Chromolaena odorata (Communist pacha),  Gynura procumbens (Longevity spinach),  Helianthus annuus (Bunga matahari),  Siegesbeckia orientalis (Common St. Paul's Wort),  Tagetes erecta (Bunga tai ayam),  Wollastonia biflora (Wedelia),  Ipomoea (Katang-katang),  Ipomoea aquatica (Kangkung),  Ipomoea batatas (Ubi jalar),  Ipomoea cairica (Ubi kates),  Ipomoea mauritiana (Akar lanar),  Ipomoea obscura (Obscure morning glory),  Ipomoea pes-caprae (Katang-katang),  Ipomoea quamoclit (Rincik bumi),  Ipomoea triloba (Three-lobe morning glory),  Jacquemontia tomentella (Akar kumiet),  Cucurbita moschata (Labu kuning),  Gynostemma pentaphyllum (Five-leaf ginseng),  Diospyros malabarica (Culiket),  Diospyros perfida (Tuba api),  Diospyros sumatrana (Kayu arang),  Diospyros wallichii (Kayu malam),  Actinodaphne borneensis (Madang),  Actinodaphne ellipticibacca (Madang),  Actinodaphne glabra (Madang),  Actinodaphne johorensis (Madang),  Actinodaphne sesquipedalis (Madang),  Cinnamomum burmannii (Kulik manih),  Cinnamomum tenuifolium (Japan cinnamon),  Cinnamomum javanicum (Kayu tuha),  Cinnamomum porrectum (Thep Taro),  Persea americana (Pokat),  Phoebe grandis (Madang silau),  Phoebe macrophylla (Madang kuning),  Abrus precatorius (Sago),  Acacia auriculiformis (Akasia),  Acacia mangium (Akasia),  Adenanthera pavonina (Sago),  Aeschynomene americana (American joint vetch),  Aeschynomene indica (Indian joint vetch),  Arachis hypogaea (Kacang tanah),  Archidendron jiringa (Jariang),  Bauhinia acuminata (Bunga kupu-kupu putih),  Bauhinia bidentata (Climbing bauhinia),  Bauhinia kockiana (Orange bauhinia),  Bauhinia purpurea (Tayuman),  Bauhinia semibifida (Butterfly climber),  Bauhinia tomentosa (Anggrek lonceng kuning),  Bauhinia variegata (Mountain ebony),  Caesalpinia crista (Kebiul),  Caesalpinia pulcherrima (Kembang merak),  Cajanus cajan (Kacang gude),  Callerya atropurpurea (Kasae),  Calliandra calothyrsus (Kaliandra),  Calopogonium mucunoides (Kalopo),  Canavalia gladiata (Kacang Koro Pedang),  Cassia fistula (Golden shower tree),  Cassia grandis (Pink shower tree),  Cassia javanica (Java cassia),  Senna siamea (Johar),  Centrosema pubescens (Butterfly pea),  Clitoria ternatea (Bunga telang),  Crotalaria incana (Shakeshake),  Crotalaria juncea (Orok-orok),  Crotalaria verrucosa (Blue rattlepod),  Desmodium heterocarpon subsp. Ovalifolium (Sweetheart),  Erythrina variegata (Dadap),  Flemingia macrophylla (Enoki-mame),  Flemingia strobilifera (Wild hops),  Glycine max (Kacang kedele),  Leucaena leucocephala (Leadtrees),  Mucuna pruriens (Kacang babi),  Pachyrhizus erosus (Bengkoang),  Parkia speciosa (Patai),  Phaseolus lunatus (Kacang lima),  Phaseolus vulgaris (Buncis),  Phyllodium pulchellum (Showy desmodium),  Pterocarpus indicus (Angsano),  Saraca indica (Pohon asoka),  Senna alata (Ketepeng cina),  Vigna radiata (Kacang hijau),  Bellucia pentamera (Jambu lelen),  Clidemia hirta (Senduduk bulu),  Melastoma malabathricum (Sikaduduak),  Memecylon acuminatissimum (Mutik),  Pachycentria constricta (Whitethorn acacia),  Pternandra azurea (Siri-siri),  Ardisia purpurea (Kayu lundong),  Aegiceras corniculatum (Black mangrove),  Ardisia elliptica (Lempeni),  Ardisia javanica (Marlberry),  Ardisia teysmanniana (Kumpang),  Citrus amblycarpa (Limau),  Citrus x aurantiifolia (Jeruk nipis),  Citrus japonica (Kumquat),  Citrus maxima (Jeruk bali),  Citrus medica (Jeruk sukade),  Citrus sinensis (Jeruk manis),  Clausena excavata (Sicerek),  Murraya paniculata (Kemuning),  Trema orientalis (Indarung)

Temporal Coverage

Start Date / End Date 1938-07-08 / 2019-11-03

Project Data

The project started in May 2019 and will end in April 2020. The aims of the project are to digitize the collections hosted at Herbarium ANDA; to prepare and establish well-managed and integrated specimen database following GBIF standard; to manage collections, locality information and specimen images; and to produce the checklist of the Flora of Sumatra. In this project, all the digitized species has also been stored in an offline database system. The participants and the main stakeholders involved in the projects consisted of students and lecturers at the Department of Biology at Andalas University, some world’s well-known herbariums including their staffs, and our domestic partner, the Indonesian Biodiversity Information Facility, as well as respected plant taxonomists working on the targeted taxa. Students and lecturers at the Department of Biology Andalas University are our main partner to provide supports for the project from within the university. Our herbarium partners participate for data verification and specimen identification. InaBIF provides us with their expertise and support for data publication.

Title Flora Sumatra: Digitizing and data basing specimens of the Sumatran Flora deposited at Herbarium Universitas Andalas (ANDA)-Part 2
Identifier BIFA4_023
Funding GBIF Grant Letter 2019 (mobilization grant), BIFA4_023
Study Area Description The main collections are from Sumatra and adjacent islands.
Design Description The information on the specimen labels is our main data source. For data collection, we conducted in three steps: data capture, data cleaning, and data publication. In the data capture process, we collected all the information on the specimen’s label, and we input the information into Microsoft Excel spreadsheets using Darwin-Core format. In this process, we grouped the specimen information into three groups, consisting of data occurrence, taxon information, and event. We save the file in csv (comma-separated values) format. We included specimen photos and scanning data into the database incorporated in associateMedia field. All the images were stored in flickr-pro media, which then will link with the filed in the dataset. We conducted data cleaning to ensure consistency and standardized data input for the dataset. We used OpenRefine for batch error handling, Canadensys tools for coordinate conversion, and Splink for coordinate verification. To verify the taxonomic nomenclature, we used resolver, iPlant collaborative, ECAT, and Plant list. All the tools we used are open-source software or available as an open online platform. Data publication includes data publishing on GBIF and scientific papers. We published all the dataset that has been cleaned and verified according to our standard on GBIF website using Integrated Publishing Toolkit (IPT) available through the link http://ipt.biologi.lipi.go.id/. After verified by GBIF, all the data will be published under the publisher Herbarium of Andalas University, available through the link https://www.gbif.org/publisher/43f4255c-f218-4a17-857a-ba3ac8456191. The data paper is written following the metadata template available in the IPT. For scientific papers, we will publish the data following the targeted journal format.

The personnel involved in the project:

Principal Investigator
Nurainas Nurainas
Metadata Provider
Ahmad Taufiq
Content Provider
Try Surya Harapan
Reviewer
Heru Handika
Curator
Syamsuardi Syamsuardi

Sampling Methods

The collecting method for the dried specimens was referred to published procedures of preparing herbarium materials (Bridson and Forman,1992). The plant materials were collected and pressed in the field then mounted on an A2 paper after the specimens were dried. Before installation into the herbarium cabinets, the specimens were put into plastic bags. Every sheet of specimens was labeled with the standard information for herbarium collections, including taxonomic identification, locality information, geo-references, collector information, and ecological data. For insect control, we freeze the specimens periodically in -20 degrees Celsius freezer for 72 hours. All of the specimens were stored in the herbarium cabinets. The storage rooms were equipped with temperature and humidity control. All of the specimens were in alphabetical orders based on the families, grouped in several groups of plants, such as dicots, monocots, ferns, and mosses.

Study Extent The collections hosted at the Herbarium ANDA were from research projects of faculties, foreign researchers, and students at the university. The collecting methods were using the standard collecting method for dried specimens. A few donated specimens were collected based on the collecting method used at the institutions from the specimen originated. The duplicates of the specimens were hosted across several herbarium, such as Bogoriense (BO), Singapore Botanical Garden (SING), and Botanical Garden of Edinburgh (E). The duplicate specimens that have not been sent were hosted at a designated room for duplicate specimens at the Herbarium ANDA. Every year, we add around 200 sheets of new specimens into the herbarium.
Quality Control We divided our working groups into two groups: a) taxonomic determination or identification group and b) data geo-referencing group. For taxonomic determination, the identification was verified by experts on the designated taxa, and also was using book references for the taxa (Ashton, 1982; Van Der Meijden, 1984; Kalkman, 1993; Shaw, 1981). The experts are writers and researchers for the area of studies and have published using the materials at the Herbarium ANDA (Utami, 2006; Hughes, 2009, 2015, Hernawati, 2006). The datum references for each coordinate were collected from the specimen labels using the WGS84 standard. If the coordinate of the locations was not recorded on the labels, we used Google Map to obtain the coordinate based on the locality information of the villages recorded on the labels.

Method step description:

  1. The information on the specimen labels is our main data source. For data collection, we conducted in three steps: data capture, data cleaning, and data publication. In the data capture process, we collected all the information on the specimen’s label, and we input the information into Microsoft Excel spreadsheets using Darwin-Core format. In this process, we grouped the specimen information into three groups, consisting of data occurrence, taxon information, and event. We save the file in csv (comma-separated values) format. We included specimen photos and scanning data into the database incorporated in associateMedia field. All the images were stored in flickr-pro media, which then will link with the filed in the dataset. We conducted data cleaning to ensure consistency and standardized data input for the dataset. We used OpenRefine for batch error handling, Canadensys tools for coordinate conversion, and Splink for coordinate verification. To verify the taxonomic nomenclature, we used resolver, iPlant collaborative, ECAT, and Plant list. All the tools we used are open-source software or available as an open online platform. Data publication includes data publishing on GBIF and scientific papers. We published all the dataset that has been cleaned and verified according to our standard on GBIF website using Integrated Publishing Toolkit (IPT) available through the link http://ipt.biologi.lipi.go.id/. After verified by GBIF, all the data will be published under the publisher Herbarium of Andalas University, available through the link https://www.gbif.org/publisher/43f4255c-f218-4a17-857a-ba3ac8456191. The data paper is written following the metadata template available in the IPT. For scientific papers, we will publish the data following the targeted journal format.

Collection Data

Collection Name Spesimen Herbarium Universitas Andalas (ANDA)
Specimen preservation methods Mounted
Curatorial Units Count 17,550 +/- 17,600 Sheet

Bibliographic Citations

  1. AKHRIADI, P., PRIMALDHI, A. and HAMBALI, M., 2008. Nepenthes naga, a new species of Nepenthaceae from Bukit Barisan of Sumatra. Reinwardtia, 12(5), pp.339-342.
  2. Ashton, P. S. 1982. Flora Malesiana. Series I-Spermatophyta. Flowering Plants Vol. 9, part 2, Dipterocarpaceae. Martinus Nijhoff. The Hague, Boston, London.
  3. Bridson, D., Forman, L. 1992. The Herbarium Handbook. Whitstable Litho Printers Ltd. Great Britain.
  4. Hernawati and Pitra A. 2006. A Field Guide to the Nepenthes of Sumatra. Nepenthes Team and PILI-NGO Movement. Bogor. Indonesia.
  5. Hughes, M., GIRMANSYAH, D. and Ardi, W.H., 2009. Seven new species of Begonia from Sumatra. Gard. Bull. Singapore, 61, pp.29-44.
  6. Hughes, M., Girmansyah, D. and Ardi, W.H., 2015. Further discoveries in the ever-expanding genus Begonia (Begoniaceae): fifteen new species from Sumatra. European journal of Taxonomy, (167).
  7. IUCN. 2018. https://www.iucnredlist.org/. Accessed in Februari 2019. Kalkman, C. (1993). Rosaceae. Flora Malesiana-Series 1, Spermatophyta, 11(2), 227-351.
  8. Kemetrian Lingkungan Hidup dan Kehutanan Republik Indonesia. Peraturan Mentri Lingkungan Hidup dan Kehutanan Republik Indonesia Nomor P.92/MENLHK/SETJEN/KUM.1/8/2018. Tentang Jenis Tumbuhan Satwa yang dilindungi.
  9. Lee, C.I.C. and Akhriadi, P., 2006. Two new species of Nepenthes (Nepenthaceae) from North Sumatra. Blumea-Biodiversity, Evolution and Biogeography of Plants, 51(3), pp.561-568.
  10. Plant List. 2019. http://www.theplantlist.org/. Accessed Februari 2019. Shaw, H. A. (1981). the Euphorbiaceae of Sumatra. Kew Bulletin, 239-374.
  11. Utami, N. 2006. Impatiens spp. (Balsaminaceae) ednemik di Sumatera dan potensi sebaaga tanaman hias. Biodiversitas. Vol. 7 (2) 2006: 135-138
  12. Van Der Meijden, R. (1984). Polygalaceae. Flora Malesiana-Series 1, Spermatophyta, 10(1), 455-539.

Additional Metadata

Purpose The aim of this project is to digitize the specimens hosted at the Herbarium ANDA, to publish a checklist of the flora of Sumatra, and to promote the database of Sumatran plant diversity.
Alternative Identifiers 39e85504-1ebe-4671-be65-19ccdc1d7c7d
http://ipt.biologi.lipi.go.id/resource?r=florasumatra-digitizing_and_data_basing_specimens_of_the_sumatran_flora_deposited_at_herbarium_universitas_andalas_part_2