Overview

The Chromosome Counts Database (CCDB) is a community resource for plant chromosome numbers. The database incorporates data from dozens of currently available sources. The main aim of CCDB is to serve as a central reference point to the vast amount of data on chromosome numbers that was gathered to date.

The database is intended as a public resource for researchers interested in acquiring plant cytological data. As such, it enables researchers to add new counts or to correct existing data entries, thereby improving data quality facilitating data sharing.


How to use CCDB?

CCDB includes 381173 entries, hierarchically ordered by taxonomic conventions. Each entry is ascribed to a plant species, genus, family and one of four major plant groups (angiosperms, gymnosperms, pteridophytes(including lycophytes) or bryophytes). Users can browse the different taxonomic levels through the Browse page. Alternatively, the search box can be used to query for specific species or genus names. See the name resolution section for further details. Data can be downloaded as CSV files at different taxonomic levels.


Taxonomic name resolution

For taxonomic name standardization, all names in the database have been resolved using Taxonome (Kluyver and Osborne 2013), an automatic taxonomic name resolution software. Given The Plant List (List 2013) version 1.1 as an underlying database for name synonymy, the software matches species names to their accepted name, while accounting for spelling differences.This is done using a two-step process where the original name is first matched to a name in the reference database, using fuzzy-matching, i.e. accounting for spelling mistakes and different taxonomic naming conventions. The matched name is then mapped to the corresponding accepted name by collapsing synonyms. When the original name is different from the intermediate matched name, this is indicated as a red exclamation mark (!) to the left of the record.
CCDB can be searched by both accepted names and synonyms. Querying by a synonym will yield counts originally reported for that synonym, while querying by an accepted name will yield all counts with name resolved to that accepted name (including its synonyms). The taxonomic status is indicated for each database entry.


Exporting Data

Users can export data to comma-separated values (CSV) files, which can be viewed using various spreadsheet applications such as Microsoft Excel. Data may be exported at species, genus and family levels. Clicking the 'Export to CSV' button will produce a table containing all records ascribed to the chosen taxon. Note that exported tables include additional information, not displayed when browsing the website. Exported files include the following columns:


Data contribution

CCDB is a community resource, and as such, researchers are invited to contribute to the completeness and correctness of the resource. This can be achieved by submitting new data, originating from resources not yet incorporated into the database as well as reporting errors found in the database. All reports and submissions will be manually inspected by the database curator. Please read the explanations below before making any contribution.


Submitting new counts

To submit new counts, follow these steps:
1. Click the Submit new counts link.
2. Fill in your details in the form. These will only be used to contact you regarding your report.
3. Download the CSV template submission file from within the form.
4. Insert your new counts in the file. You can include one or more counts. Each count will be represented by a row in the CSV file, and should include the following fields:


See the example CSV, which can also be downloaded from within the form.
5. Upload the CSV to the form and click the 'Submit' button.


Reporting errors

CCDB was established mainly by automatic parsing of various data resources. Our general approach was to maximize retrieval accuracy rather than data completeness. However, some inaccuracies in taxa names and chromosome numbers may still occur, especially in cases where OCR was involved in the process.

To report an error, follow these steps:
1. Click the Report counts link.
2. Fill in your details in the form. These will only be used to contact you regarding your report.
3. Download the CSV template.
4. Insert your error reports in the file. You can include one or more data entries. Each erroneous entry should be represented by a row in the CSV file. You will have to supply the database entry ID for which you want to report an error. To obtain the ID, download the chromosome counts (using the 'Export to CSV' button) from the corresponding web page, and provide the database ID ('id' column). Next, you have to describe the error and provide the correct value. Common errors may include a taxon name inaccuracy, a taxonomic mistake or erroneous chromosome number. Please provide a clear and simple explanation of the error you are reporting.
See the CSV example.
5. Upload the CSV to the form and click the 'Submit' button.


Resource list

CCDB incorporates chromosome counts obtained from a large number of electronic resources, older chromosome-counts compendiums in the form of printed books, and an array of miscellaneous sources such as floras, monographs, and other scientific manuscripts. Each resource was parsed and inserted into CCDB using a resource-specific manner, as described below.


Online databases

Resource Name: Plant DNA C-values database (C-values database)
Description: Created and maintained by the Royal botanic garden, Kew, this database includes C-value and chromosome count data for plants of all major groups. Data were obtained via personal communication, as CSV files.
Number of entries: 6185
Reference: Kew RB, Gardens VK, Wakehurst V. Plant DNA C-values Database. 2012.


Resource Name: Chromosome number database of Polish plants (Poland Database)
Description: Contains mainly chromosome numbers determined for plants from the area of Poland, obtained by Polish botanists in the years 1950-1990. Data were obtained via personal communication, as CSV files.
Number of entries: 2165
Reference: Góralski G, Lubczyńska P, Joachimiak AJ. Chromosome number database.


Resource Name: Karyological database of the genus Cardamine (Cardamine)
Description: Contains chromosome numbers for 101 taxa of the genus Cardamine (Brassicaceae).
Number of entries: 2782
Reference: Kučera J, Valko I, Marhold K. On-line database of the chromosome numbers of the genus Cardamine (Brassicaceae). Biologia (Bratislava). 2005;60(4):473-6.


Resource Name: Index to Plant Chromosome Numbers (IPCN) (IPCN online)
Description: includes chromosome numbers for plants of all taxonomic groups. The database includes counts originally published in the printed version of the index from 1979 onward. Data were retrieved using the web API and Perl scripts.
Number of entries: 109696
Reference: Goldblatt P, Johnson DE. Index to plant chromosome numbers. Missouri Botanical Garden; 1981.


Resource Name: Chilean Plants Cytogenetic Database (Chilean Cytogenetic Database)
Description: An online database containing cytological data for 163 Chilean plant species. Data were directly downloaded and parsed from the HTML page.
Number of entries: 216
Reference: Jara-Seguel P, Urrutia J. Chilean plants cytogenetic database. 2011.


Resource Name: CHROBASE - Chromosome numbers for the Italian flora (CHROBASE)
Description: Stores chromosome counts mainly for the Italian and Corsican flora. Data were obtained by automatically parsing the HTML pages of the database.
Number of entries: 6358
Reference: Bedini G, Garbari F, Peruzzi L. onwards. Chrobase. it. Chromosome numbers for the Italian flora.


Resource Name: Botanical Society of the British Isles (BSBI) cytology database (British Isles cytology)
Description: Includes information about vascular plants and Charophytes native and alien to the British Isles. Data were obtained by automatically parsing the HTML pages of the database.
Number of entries: 2746
Reference: http://rbg-web2.rbge.org.uk/BSBI/cytsearch.php


Resource Name: Index to chromosome numbers in Asteraceae (Asteracea)
Description: An extensive database of chromosome counts in the Asteraceae family, maintained by Kobe university. Data were obtained by automatically parsing the HTML pages of the database.
Number of entries: 22822
Reference: Watanabe K. Index to chromosome numbers in Asteraceae. 2002.


Resource Name: Published chromosome-counts in Hieracium (Hieracium)
Description: A literature survey of the chromosome numbers of the genus Hieracium. Data were directly downloaded and parsed from the HTML page.
Number of entries: 316
Reference: Schuhwerk F. Published chromosome counts in Hieracium. 1996.


Resource Name: ChromoPar – Paraguay chromosome counts database (ChromoPar)
Description: Chromosome numbers of vascular plants, published in the Flora of Paraguay. Data were obtained by direct download of the provided PDF files, conversion to text format, and automatic parsing.
Number of entries: 1263
Reference: http://www.ub.edu/botanica/cromopar/basedato.htm


Resource Name: Karyological database of the ferns and flowering plants of Slovakia (Slovakia Database)
Description: Includes data for ferms and flowering plants of the wild and cultivated flora of Slovakia. This is an online version of the publication Chromosome number survey of the ferns and flowering plants of Slovakia (Marhold et al. 2007). Data were obtained by automatically parsing the HTML pages of the database.
Number of entries: 7463
Reference: Marhold K, editor. Chromosome number survey of the ferns and flowering plants of Slovakia. Veda; 2007.


Resource Name: DCDB- Delphineae Chromosome Database
Description: Created and maintained by the BioC-GReB, Equip de Recerca en Biologia de la Conservació de Plantes/Dipòsit Digital de la Universitat de Barcelona. Data were obtained via personal communication, as CSV files.
Number of entries: 1459
Reference: Bosch, M., J. Simon, J. López-Pujol & C. Blanché (2016) - DCDB: an updated on-line database of chromosome numbers of tribe Delphinieae (Ranunculaceae) - BioC-GReB, Equip de Recerca en Biologia de la Conservació de Plantes/Dipòsit Digital de la Universitat de Barcelona
http://hdl.handle.net/2445/98702


Hard-copy chromosome number compendiums

Data from printed books containing chromosome counts indexes was obtained as follows. First, the books were scanned to obtain image files. Second, using the OCR tool of Adobe Pro the files were converted to textable PDF files. We used ‘Some PDF to Text Converter’ to convert the PDF files into plain text files that could be parsed automatically using Python scripts. The following sources were retrieved this way:


Resource Name: Chromosome numbers of northern plant species (Love, 1948)
Number of entries: 892
Reference: Löve Á, Löve D. Chromosome numbers of northern plant species. Reykjavík: Ingólfsprent; 1948. University Institute of Applied Sciences.


Resource Name: Chromosome atlas of flowering plants (Darlington, 1955)
Number of entries: 11905
Reference: Darlington CD, Wylie AP. Chromosome atlas of flowering plants. Chromosome atlas of flowering plants.. 1956. George Allen and Unwin Ltd., London, UK


Resource Name: Cytotaxonomical atlas of the Pteridophyta (Love, 1977)
Number of entries: 4050
Reference: Love A, Love D, Pichi Sermolli RE. Cytotaxonomical atlas of the Pteridophyta. Vaduz: J. Cramer 398p.-Chrom. nos.. Chromosome numbers. Geog. 1977. Vaduz Liechtenstein, J. Cramer.


Resource Name: Chromosome numbers of flowering plants (Fedorov, 1974)
Number of entries: 25804
Reference: AnA F. Chromosome numbers of flowering plants. Academy of Sciences of the USSR. Komarov Botanical Institute, Leningrad (Reprint 1974). 1969.


Resource Name: Flora Europaea – check list and chromosome index (Flora Europaea)
Number of entries: 4453
Reference: Moore DM. Flora Europaea check-list and chromosome index. Cambridge University Press; 1982.


Resource Name: Chromosome atlas of flowering plants of the Indian subcontinent; volumes 1 and 2 (Kumar, 1987)
Number of entries: volume 1: 7170 , volume 2: 4309
Reference: Kumar V, Subramaniam B. Chromosome atlas of flowering plants of the Indian subcontinent. Volume 1. Dicotyledons. Calcutta: Botanical Survey of India,(1987) xxvi, 464p.-. En Chromosome numbers. Geog. 1988;6.


Resource Name: Index to plant chromosome numbers for 1965 (IPCN65)
Number of entries: 3766
Reference: Ornduff R. Index to plant chromosome numbers for 1965. Regnum Vegetabile 50.


Resource Name: Index to plant chromosome numbers for 1966 (IPCN66)
Number of entries: 3717
Reference: Ornduff R. Index to plant chromosome numbers for 1965. International Bureau for Plant Taxonomy and Nomenclature of the International Association for Plant Taxonomy.


Resource Name: Index to plant chromosome numbers for 1967-1971 (IPCN67-71)
Number of entries: 20886
Reference: Moore RJ. Index to plant chromosome numbers for 1969. Utrecht: IAPT 112p.(Regnum Vegetabile vol. 77). Geog. 1971.


Resource Name: Index to plant chromosome numbers for 1972 (IPCN72)
Number of entries: 3473
Reference: Moore RJ. Index to plant chromosome numbers for 1972. Utrecht: International Bureau for Plant Taxonomy and Nomenclature 110p.(Regnum Vegetabile, vol. 91). Geog. 1974.


Resource Name: Index to plant chromosome numbers for 1973-1974 (IPCN73-74)
Number of entries: 9904
Reference: Moore RJ. 1977. Index to plant chromosome numbers for 1973/74. Regnum Vegetabile.


Resource Name: Index to plant chromosome numbers for 1975-1978 (IPCN75-78)
Number of entries: 12146
Reference: Goldblatt P. Index to plant chromosome numbers 1975-1978. St. Louis: Missouri Botanical Garden vii, 553p.(Monographs in Systematic Botany vol. 5)-. En Chromosome Surveys (KR, 198110215). 1981.
Description: counts were inserted into the database only in case the online IPCN database did not already contain these counts.


Resource Name: Index to plant chromosome numbers for 1956
Number of entries: 1645
Reference: Cave, M. S. 1958. Index to Plant Chromosome Numbers for 1956. California Botanical Society, Berkeley.
Description: Data from the Marion Cave chromosomal indices (1956 – 1964, plus supplement), were scanned by the Herbarium at Ohio State University (OS), and were included in CCDB using a dedicated python script.


Resource Name: Index to plant chromosome numbers Supplement - Previous to 1956
Number of entries: 1641
Reference: Cave, M. S. 1959. Index to Plant Chromosome Numbers for 1956 Supplement. California Botanical Society, Berkeley.
Description: Data from the Marion Cave chromosomal indices (1956 – 1964, plus supplement), were scanned by the Herbarium at Ohio State University (OS), and were included in CCDB using a dedicated python script.


Resource Name: : Index to plant chromosome numbers for 1957
Number of entries: 1656
Reference: Cave, M. S. 1958. Index to Plant Chromosome Numbers for 1957. California Botanical Society, Berkeley.
Description: Data from the Marion Cave chromosomal indices (1956 – 1964, plus supplement), were scanned by the Herbarium at Ohio State University (OS), and were included in CCDB using a dedicated python script.


Resource Name: Index to plant chromosome numbers for 1958
Number of entries: 1812
Reference: Cave, M. S. 1959. Index to Plant Chromosome Numbers for 1958. California Botanical Society, Berkeley.
Description: Data from the Marion Cave chromosomal indices (1956 – 1964, plus supplement), were scanned by the Herbarium at Ohio State University (OS), and were included in CCDB using a dedicated python script.


Resource Name: Index to plant chromosome numbers for 1959
Number of entries: 1367
Reference: Cave, M. S. 1960. Index to Plant Chromosome Numbers for 1959. California Botanical Society, Berkeley.
Description: Data from the Marion Cave chromosomal indices (1956 – 1964, plus supplement), were scanned by the Herbarium at Ohio State University (OS), and were included in CCDB using a dedicated python script.


Resource Name: Index to plant chromosome numbers for 1962
Number of entries: 2576
Reference: Cave, M. S. 1963. Index to Plant Chromosome Numbers for 1962. California Botanical Society, Berkeley.
Description: Data from the Marion Cave chromosomal indices (1956 – 1964, plus supplement), were scanned by the Herbarium at Ohio State University (OS), and were included in CCDB using a dedicated python script.


Resource Name: Index to plant chromosome numbers for 1963
Number of entries: 3631
Reference: Cave, M. S. 1964. Index to Plant Chromosome Numbers for 1963. California Botanical Society, Berkeley.
Description: Data from the Marion Cave chromosomal indices (1956 – 1964, plus supplement), were scanned by the Herbarium at Ohio State University (OS), and were included in CCDB using a dedicated python script.


Floras

Resource Name: eFlora (eFlora)
Description: A vast collection of online floras from different geographical regions, including free-text description cards for plant taxons. Data were obtained by automatically searching the text for chromosome counts, using a dedicated Perl script.
Number of entries: 11278
Reference: http://www.efloras.org


Resource Name: Flora Iberica (Flora Iberica)
Description: A catalog of the wild flora of vascular plants in the Iberian Peninsula and Balearic islands. Data were obtained by automatically parsing the web pages, including species descriptions and chromosome numbers.
Number of entries: 9450
Reference: http://www.floraiberica.es/


Resource Name: Interactive flora of NW Europe (flora of NW Europe)
Description: Part of the World Biodiversity Database, the project encompasses more than 3500 taxa and includes all natives, all naturalized plants, all crop plants and all recurrent casuals of North-Western Europe. . Data were obtained by automatically searching for chromosome numbers through the taxa cards.
Number of entries: 2762
Reference: http://wbd.etibioinformatics.nl/bis/flora.php


Resource Name: Karyological knowledge of the Catalan vascular flora inferred from “CromoCat” database
Description: Created and maintained by Joan Simon & Cesar Blanche at "Universitat de Barcelona".
Data were obtained via personal communication, as CSV files. Data is available at BDBC/Flora
Number of entries: 33772
Reference: J. SIMON & C. BLANCHÉ, Karyological knowledge of the Catalan vascular flora inferred from “CromoCat” database. 2016.


Manuscripts and Monographs

Scientific manuscripts that contain large amounts of chromosome counts, as well as several Systematic Botany monographs were parsed in a source-specific manner, using tailored Perl or Python scripts. The following publications were used:


Resource Name: Systematic Botany monographs (Sys Bot Monographs)
Description: Nine monographs, published in Systematic Botany, were automatically parsed to obtain chromosome counts.
Number of entries: 351
Reference:


Other resources

Resource Name: IAPT/IOPB chromosome data (IAPT/IOPB)
Description: Chromosome numbers published through IAPT Taxon between the years 2006 and 2016. Data were downloaded as PDF documents, converted to text files using ‘Some PDF to Text Converter’, and then parsed using a dedicated Perl and Python scripts.
Number of entries: 5005
Reference: Baltisberger, M. & Voelger, M. 2006. Sternbergia sicula. In: Marhold, K. (ed.), IAPT/IOPB chromosome data 1. Taxon 55: 444, E2, http://www.iopb.org Marhold K. IAPT/IOPB chromosome data 1. Taxon. 2006 May 1:443-5.


Resource Name: Chromosome numbers of indigenous New Zealand plants (Dawson New Zealand)
Description: Obtained as a CSV file via personal communication from Murray Dawson.
Number of entries: 2175


Resource Name: Chromosome numbers for Solanaceae species (Goldberg, pers comm)
Description: Obtained as a CSV file via personal communication from Emma Goldberg.
Number of entries: 1968


Resource Name: Chromosome numbers of ferns (Barker, pers comm)
Description: Obtained as a CSV file via personal communication from Michael Barker. Counts were inserted to the database only if they were not already included in the data downloaded from the IPCN website.
Number of entries: 197
Reference: Wood, Troy E., et al. "The frequency of polyploid speciation in vascular plants."Proceedings of the national Academy of sciences 106.33 (2009): 13875-13879.


Resource Name: Veronic
Description:
Number of entries: 2431
Reference:


Resource Name: Documented chromosome number checklist of Austrian vascular plants
Description:
Number of entries: 5700
Reference:


Resource Name: Original-count
Description: Counts that were reported to CCDB by individual researchers.
Number of entries: 52



How to cite

Rice, A., Glick, L., Abadi, S., Einhorn, M., Kopelman, N. M., Salman-Minkov, A., Mayzel, J., Chay, O. and Mayrose, I.
The Chromosome Counts Database (CCDB) – a community resource of plant chromosome numbers. New Phytologist (2014). doi: 10.1111/nph.13191
Abstract