AVH Restricted Help Page

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Contents

Introduction

The Australia's Virtual Herbarium (AVH) portal allows users to access herbarium specimen information from all Australian Commonwealth, state and territory herbaria with a single query. Data returned by the AVH portal is presented to the user as it is delivered to AVH by the participating herbaria, including uncertainties and errors, and should be checked for accuracy and precision before use.

The most common errors in AVH data arise from the misidentification of specimens or incorrect locality geocodes. Much of the data provided through AVH has been acquired for use in plant taxonomy and systematics and, while suitable for these purposes, may not be suitable for applications that require higher levels of precision. Data is continually tested and improved at the herbaria, and is regularly updated in AVH. The contributing herbaria appreciate feedback on any errors or discrepancies detected in the data.

The herbaria have agreed to provide the following information for this version of AVH: taxonomic information, herbarium code and accession number, collector name, collecting number, collecting date, generalised locality, state, country, geocode, geocode source and geocode precision. Some herbaria deliver additional fields.

It is important to bear in mind that different herbaria store their collection data in different ways. Furthermore, different herbaria, and indeed botanists in the same herbarium, delimit certain taxa in different ways. Therefore, queries will often return surprising results and it will not always be possible to get all the data the user is after with one query.

The information on this page is intended to assist users in understanding the limitations of AVH data and to achieve the best query results.

Herbarium abbreviations

Throughout the help page, the following codes are used to refer to the participating herbaria:

AD – State Herbarium of South Australia
BRI – Queensland Herbarium
CANB – Australian National Herbarium
DNA – Northern Territory Herbarium
HO – Tasmanian Herbarium
MEL – National Herbarium of Victoria
NSW – National Herbarium of New South Wales
PERTH – Western Australian Herbarium

Query form

General

AVH search terms are case insensitive: 'Banksia' and 'banksia' will return the same records.

The wildcard is '%'. 'alb%' will return 'alba', 'album', 'albida', 'albidum', 'albescens', 'albertensis' etc. The wildcard can be placed anywhere in the search value to make the desired pattern. A wildcard at the start of a query value will significantly slow down a search and may result in the query timing out.

Navigating the query form

The query form works best with Javascript enabled, but will also work without. The following assumes that Javascript is enabled.

The restricted access query form contains two expandable sections in which search criteria can be selected: one for taxon names and one for additional search criteria. Typing a genus name in the taxon name query or selecting a search criterion from the list in the extended query will bring up a plus-sign button. Clicking on the button or hitting <ENTER> when it is in focus will add a new row. Up to five taxon names can be entered. The number of extended search criteria that can be entered is limited by the number of options in the drop-down list.

The query form can be navigated using the mouse, entirely with the keyboard, or a combination of the two. In order to navigate within the list boxes using your keyboard in Internet Explorer, you need to press <ALT+(arrow down)> (or <ALT+(arrow up)>) first. The list will then open as if you clicked on it with the mouse and you can navigate through the list using the up and down arrows or by starting to type the query term. In Firefox you can navigate with the up and down arrows or by typing, but you only get to see one line at a time. Pressing <ALT+(arrow down)> first will open the list so you can see all options at the same time. In Google Chrome, Safari and Opera you can navigate the lists as in Firefox, but you cannot open the list with the keyboard.

Taxonomy

Taxon name

You can query up to five taxon names at a time. Note that different herbaria may delimit certain taxa in different ways, so you may need to also query on synonyms in order to retrieve all records of a taxon. For example, some herbaria still recognise the genus Dryandra, while in other herbaria Dryandra is merged with Banksia. So, for instance, if you want to retrieve all records of the species Banksia armata (or Dryandra armata, as the case may be), you should include both names in your query.

The following resources provide authoritative information on plant names and synonymy:

The Australian Plant Census (APC) is a cooperative project under the auspices of the Council of Heads of Australasian Herbaria Inc. (CHAH). The APC will provide a compromise view of Australian taxa, as well as an overview of different taxonomies and full synonymies. Once completed, an APC-based name service will be incorporated in AVH, allowing users to search for records of taxa without having to query for multiple names.

Uncertain identifications

If there is doubt about the identification of a plant, the record might contain one of the following qualifiers:

  • aff. = akin to or bordering
  • cf. = compare with
  • forsan = perhaps
  • near = close to
  •  ? = uncertain
  • incorrect = incorrect (this is used where the name applied to the specimen is known to be incorrect, but a new, positive identification has not yet been made)

Selecting 'all' will include all of the above types of uncertain identifications in your query, except for 'incorrect'.

Qualifier data is currently provided by AD, CANB, HO, MEL and PERTH. Records from other herbaria may include uncertain identifications, but these do not have qualifiers.

Batch file search

The batch file search allows users to query for more taxa than the search limit provided by the form.

Files can contain genus, species, infraspecific_rank and infraspecific_epithet data in either comma-delimited or space-delimited format. Column headers are not required. The file can also include comments, as long they are prefixed by a '#' character on each line. Comma and space delimiters cannot be used together in the same file. Note that the infraspecific rank must be one of the following values, and must include a full stop.

  • subsp.
  • var.
  • subvar.
  • f.
  • subf.

For example:

genus1

genus2, species2

genus3, species3, infraspecific_rank, infraspecific_epithet

OR

genus1

genus2 species2

genus3 species3 infraspecific_rank infraspecific_epithet

When combined with other query terms, names entered in the taxon names search will be added to the list, while values entered in extended query fields will be used to restrict the scope of the query.

Family

Australian herbaria use different supra-generic classifications. Because the delimitation of families may differ between classifications, a query for a family may return different sets of genera from different herbaria. The APC will include a family classification. Until the APC has been completed and incorporated in AVH, or if you have a family concept different from the APC's, you are better off searching for a set of generic names. Supra-generic classification of cryptogams is in a state of flux and hence a query for a cryptogam family will likely yield unreliable results.

The vascular plant classification systems currently used by each herbarium are as follows:

  • State Herbarium of South Australia (AD): Engler and Prantl (with modifications) for vascular plants
  • Queensland Herbarium (BRI): APGII for angiosperms; Flora of Australia vol. 48 for pteridophytes
  • Australian National Herbarium (CANB): Cronquist for angiosperms; Dahlgren et al. for monocots; Brummitt for gymnosperms; various for pteridophytes
  • Northern Territory Herbarium (DNA): Mabberley's Plant-Book for vascular plants
  • Tasmanian Herbarium (HO): Cronquist for angiosperms; Flora of Australia vol. 48 for pteridophytes and gymnosperms
  • National Herbarium of Victoria (MEL): Cronquist for angiosperms; Flora of Australia vol. 48 for pteridophytes; internal system for gymnosperms
  • National Herbarium of New South Wales (NSW): Dahlgren for angiosperms (gradually moving to modified APGII); Crabbe et al. for ferns; Flora of Australia vol. 48 for conifers and cycads; Schuster for bryophytes
  • Western Australian Herbarium (PERTH): Cronquist (with modifications) for angiosperms (for more information on PERTH's system see: Paczkowska and Chapman (2000))

See the following references for more information on the different classification systems:

  • The Angiosperm Phylogeny Group (2003). An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II. Botanical Journal of the Linnaean Society 141, 399–436.
  • Brummitt, R.K. (1992). Vascular plant familes and genera. Royal Botanic Gardens, Kew.
  • Crabbe, J.A., Jermy, A.C. and Mickel, J.T. (1975). A new generic sequence for the pteridophyte herbarium. British Fern Gazette. 11, 141–162.
  • Cronquist, A. (1981). An integrated system of classification of flowering plants. Columbia University Press, New York.
  • Dahlgren, R.M.T. (1975). A system of classification of angiosperms to be used to demonstrate the distribution of character. Botaniska Notiser 128, 199–147.
  • Dahlgren, R.M.T., Clifford, H.T. and Yeo, P. (1985). The families of the monocotyledons: structure, evolution, and taxonomy. Springer, Berlin.
  • Engler, A. (ed.) (1924). Die Naturlichen Pflanzenfamilien: nebst ihren Gattungen und wichtigeren Arten insbesondere den Nutzpflanzen, 2nd edn. Engelmann, Leipzig.
  • George, A.S. (ed.) (1999). Flora of Australia, vol. 1, Introduction, 2nd edn. Australian Biological Resources Study, Canberra/CSIRO, Melbourne.
  • Jermy, A.C., Crabbe, J.A. and Thomas, B.A. (1973). The phylogeny and classification of the ferns. Academic, London.
  • Kubitzki, K. (ed.) (1990). The families and genera of vascular plants, vol. 1, Pteridophytes and gymnosperms. Springer-Verlag, Berlin.
  • Mabberley, D.J. (2008). Mabberley's Plant-Book: a portable dictionary of the higher plants, their classification and uses, 3rd edn. Cambridge University Press.
  • Orchard, A.E. (ed.) (1998). Flora of Australia, vol. 48, Ferns, gymnosperms and allied groups. Australian Biological Resources Study, Canberra/CSIRO, Melbourne.
  • Paczkowska, G. and Chapman, A.R. (2000). The Western Australian flora: a descriptive catalogue. Western Australian Herbarium, Perth, pp. 8–9.
  • Schuster, R.M. (1984). New manual of bryology. Hattori Botanical Laboratory, Japan.
  • Singh, G. (2004). Plant systematics: an integrated approach. Science Publishers, New Hampshire.

Scientific name

The scientific name includes the authorship. If you do not know the author of a name, or don't wish to include it, use a wildcard (%). For a list of standard author abbreviations, see the International Plant Names Index Author Query.

Determined by

The currently accepted determination is provided. For the most effective search, enter the surname of the determiner with a wildcard (%) either side, e.g. '%walsh%'.

Determination information is currently provided by AD, BRI, CANB, NSW and PERTH.

Determination date

Querying on determination date will currently only return records that have a complete determination date recorded (i.e. day, month and year), regardless of whether you query on a complete date or a partial date.

Determination date is currently provided by AD, CANB, NSW and PERTH.

Geography

The location component of the query can be specified in a number of ways. Varying degrees of confidence and uncertainty are associated with the locality fields. Some fields have been filled in in error by the collector; other fields have been completed by other people after the event; others have been automatically generated; others are the result of historical interpretation, and others have changed through geopolitical adjustments.

Country

Country can either be selected from the drop-down menu or typed in the country query box. Note that many herbaria only deliver Australian records to AVH, and some herbaria that do provide ex-Australian records deliver geographical regions in this field rather than ISO country names (see TDWG World Geographical Scheme for Recording Plant Distributions). Also, changes in geopolitical boundaries mean that the country recorded as the collecting location for some older specimens may not correspond to the country that the locality is mapped in today.

State

The state or territory can be typed in the state query box or, if you have already selected a country, it can be chosen from the drop-down menu. You can select more than one state from the drop-down menu by holding the <CTRL> or <SHIFT> key when selecting the states. Note that querying by state in countries other than Australia may give inaccurate results, as some herbaria deliver geographical regions rather than country and state names (see TDWG World Geographical Scheme for Recording Plant Distributions).

Herbarium region

This field allows you to query by a botanical or geographic region. As different herbaria apply different herbarium regions to their specimen records, it is best to use this query term when searching for records from a single herbarium. Please contact individual herbaria if you require information on the herbarium regions used.

Near named place

The near named place to the locality of the collection, generally based on Geoscience Australia’s 1:100 000 topographic maps.

Near named place is currently provided by AD, BRI, CANB, DNA, HO, MEL and PERTH.

Locality text

You can query for terms that occur within the textual locality information associated with herbarium specimens. To query this field most effectively, enter a search term with a wildcard (%) either side, e.g. '%simpson desert%'. Querying by locality works best in combination with other search criteria.

Bounding box query

The range query allows you to query for records within a bounding box defined by a range of latitude and longitude. When entering decimal coordinates, use negative values for southern latitudes and western longitudes, and ensure that the lower latitude and longitude values are entered first.

Geocode precision

The radius in metres within which the coordinates assigned to a record are estimated to be accurate. For example, a record with a geocode precision of 10,000 will have been collected within a 10 km radius of the geocode assigned to that collection.

Some herbaria assign precision ratings as classes rather than absolute values. Because of this, users should be cautious when querying by geocode precision as the results may be misleading. For example, MEL assigns precision classes of 0–50 m, 51–1000 m, 1001–10,000 m, 10,001–25,000 m and 25,001–50,000 m. A query for records with a geocode precision higher than 5000 m will only return records in the higher precision classes (0–50 m and 51–1000 m), and will omit records in the 1001–10,000 m class that may in actuality have been collected within 5000 m of the geocode.

Geocode source

An indication of whether the geocode was provided by the collector, assigned by the database compiler, automatically generated from a stated locality, or generated from the nearest named place (generalised arbitrary point).

Collecting data

Collector

The name of the primary collector. For a more effective search, enter the surname of the collector with a wildcard (%) either side, e.g. '%beauglehole%'. Querying by collector works best in combination with other search criteria.

Collecting number

This is the sequential number (or other codified number) that is given to the specimen by the primary collector(s). Components of a number that have been interpreted will appear in brackets. If the collection number is not recorded or not known, this field will be populated with 's.n.' (sine numero).

Additional collectors

Additional collectors responsible for the collection of the specimen from the wild. For a more effective search, enter the surname of the collector with a wildcard (%) either side, e.g. '%bean%'. Querying by additional collectors works best in combination with other search criteria.

Collecting date

Querying on collecting date will currently only return records that have a complete collecting date recorded (i.e. day, month and year), regardless of whether you query on a complete date or a partial date.

Altitude

The altitude, or the altitudinal range, at which a specimen was collected. Note that altitude is usually only recorded where the altitude of the collecting locality was provided by the collector, although some herbaria have attempted to retrofit altitudes to specimens using digital elevation models and spatial information systems. Altitude is recorded for approximately 15 per cent of collections, so a lack of records returned when querying this field does not necessarily equate to a lack of records collected at that altitude.

Altitude data is currently provided by AD, BRI, CANB, HO, MEL and NSW.

Depth

The water depth at which an algal or aquatic specimen was collected. Note that depth is only recorded where the depth of the collecting site was provided by the collector (depth is recorded for approximately 20 per cent of algae and sea grass collections), so a lack of records returned when querying this field does not necessarily equate to a lack of records collected at that depth.

Depth data is currently provided by AD, BRI, CANB, MEL and NSW.

Cultivated plants

Where specimen records are flagged as 'cultivated' by the source herbarium, they will, by default, be excluded from your query. Check the box if you wish to include cultivated plant records in your query. Make sure you check the 'Cultivated flag' box under 'Display options' to include cultivated status in the results.

Please note that the effectiveness of the exclude/include cultivated plant records function is dependent on whether cultivated plant records are provided, and flagged as cultivated, by each herbarium. Because cultivated plant records are dealt with in a variety of ways by different herbaria, query results may include cultivated plant records even if you chose to exclude them. While the participating herbaria intend to standardise the way that cultivated plant records are delivered to the AVH, this requires a lot of work and is impractical at present. If accurate cultivated status data is critical for your research, you should clarify any suspect results with individual herbaria.

  • AD is providing cultivated plant records, along with their cultivated status
  • BRI is not providing cultivated plant records
  • CANB is providing cultivated plant records, along with their cultivated status
  • DNA is providing cultivated plant records. Newer records will include a cultivated status, but older records do not. DNA does not geocode cultivated plant records, so they will only appear in data tables, not in maps.
  • HO is providing cultivated plant records, but not cultivated status. Records of non-native cultivated plants are geocoded, but those of native taxa are not.
  • MEL is not providing cultivated plant records
  • NSW is providing cultivated plant records, along with their cultivated status
  • PERTH is providing cultivated plant records, but not cultivated status. The vast majority of PERTH's cultivated plant records are not geocoded, so they will only appear in data tables, not in maps.

Curation

Specimen located at

You can restrict your results to specimens held at a particular herbarium.

For specimens at the Australian National Herbarium (CANB), you can choose to query the Canberra Botanic Gardens (CBG) collection (which was united with CANB, formerly Herbarium Australiense, in 1993), the main CANB collection, or both.

Accession number

The accession number is the unique identifier of a specimen within a herbarium. If you are looking for a specific collection and you know its accession number you can enter it here. To avoid getting records from other herbaria in your results you should also enter the herbarium in the previous field.

Note the following prefixes and suffixes apply:

  • BRI – all BRI accession numbers are prefixed by 'AQ', which must be included in the query.
  • CANB – divided mixed collections have been given suffixes 'a', 'b', etc. The recent practice is to append a sequential decimal number.
  • DNA – accession numbers are prefixed with either 'D' – Darwin or 'A' – Alice Springs. More recent (since 2007) and future accessions will be 'D' numbers.
  • MEL – accession numbers are succeeded by a letter that distinguishes individual components of a mixed collection (i.e. where more than one taxon or more than one collection appears on the same sheet or in the same packet, and cannot be separated). 'A' is the default suffix for all collections; 'B', 'C' etc. indicate additional components. Enter the appropriate suffix after the accession number (with no space between). If you don't know which component you're after, or if you wish to view all components, use the wildcard character (%).

Record update date

The date that the record was last updated at the host institution.

This data is currently provided by AD, CANB, DNA, HO, MEL, NSW and PERTH.

Output

Map

Mapping specimen records can provide a good overview of species' distributions. Only georeferenced records are shown on maps; to access non-geocoded records, choose another output format. The number of records from each herbarium is displayed in the top right of the screen. Note that these numbers include records that do not have latitude and longitude recorded. Click on the 'Redraw map' button after changing any display options. Clicking on 'New query' will take you back to the query page.

If the legend has more than one item, you can turn individual layers on and off. The map and legend can be downloaded in various formats.

You can open an overview map by clicking on the arrow in the lower right corner of the map. Clicking anywhere in the overview map will reposition the map. Clicking on the arrow in the overview map will close the overview map.

Boxes can be dragged to different positions, and minimised and then restored. The legend and query boxes can be resized as well. Clicking on the 'Reset boxes' button will return all elements to their original position. Note that the 'Reset boxes' button will only appear after you have moved, resized or minimised a box.

The results can be grouped in different ways:

  • By species – if more than one species is mapped, each species is displayed with a different symbol.
  • By taxon – if more than one taxon is mapped, each species or infraspecific taxon is displayed with a different symbol.
  • By herbarium – records from different herbaria are displayed with a different symbol.
  • By precision – records are displayed according to the precision assigned to the latitude and longitude.
  • Use single symbol – all records are displayed with the same symbol.

You can select one of the following options:

  • Show specimen information – the specimen data associated with the record will be displayed in a separate window.
  • Pan – click on the map (don't drag it) to reposition.
  • Zoom out – click on the map to zoom out by the factor entered under zoom factor.
  • Zoom in – click on the map to zoom in by the factor entered under zoom factor.

The following layers can be displayed on the map. The terrain, temperature and rainfall layers cannot be displayed together.

  • Terrain – general terrain features developed by Geoscience Australia, National Mapping Division. This layer is not available when zooming in at higher magnifications.
  • Temperature – mean annual maximum temperature isotherms from base climatological data sets supplied by the Bureau of Meteorology.
  • Rainfall – mean annual rainfall isohyets from base climatological data sets supplied by the Bureau of Meteorology.
  • States – state and territory borders, derived from Global Map Data Australia 1M 2001 developed by Geoscience Australia, National Mapping Division.
  • IBRA regions – the Interim Biogeographic Regionalisation of Australia regions, which categorise the Australian continent into regions with similar geology, landform, climate, vegetation and fauna.
  • 10° graticule – latitude and longitude grid at 10° intervals.

HTML table

You can choose to display 10, 25, 50 or 100 records per page. Use the navigation buttons at the right of the table header to move through the results pages. The scroll bar at the bottom of the table allows you to view the fields that don't fit within the table window.

By default, your query results will be ordered by herbarium and accession number. The data can be sorted by clicking on the arrows next to the column. Click on the arrows once to sort the results in ascending order; click twice to sort in descending order. You can sort on up to three columns at once by holding the <SHIFT> key while selecting the second and third columns.

Note that, because some accession numbers include letters, the accession numbers are treated as text and can not be ordered numerically.

Output to data file

You can choose to output your query results as a comma delimited file (CSV), in ABCD format or in HISPID3 format. Files can either be downloaded or sent as a zip file to an email address.

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