AVH Restricted Help Page

From HISCOM

Contents 1 Introduction 1.1 Herbarium abbreviations 2 General 3 Plant name 3.1 Family 3.2 Qualifiers 3.3 Bulk searching 4 Determination 5 Location 5.1 Country 5.2 State 5.3 Botanical region 5.4 Nearest named place 5.5 Locality text 5.6 Altitude 5.7 Depth 5.8 Geocode precision 5.9 Geocode source 5.10 Range query 5.11 Centroid query 6 Collection 6.1 Collector 6.2 Collecting number 6.3 Additional collectors 6.4 Specimen located at 6.5 Accession number 6.6 Cultivated records 7 Collection date 7.1 Date range query 8 Curation 8.1 Duplicate specimens at 8.2 Loan job number 8.3 Loan item (specimen) number 8.4 Exchange job number 8.5 Exchange item number 8.6 Donor 8.7 Donor accession number 8.8 Type 8.9 Validation level 8.10 Record creation date 8.11 Record update date

Introduction

The Australia's Virtual Herbarium (AVH) application enables a single query to access specimen records from all the Australian Commonwealth, State and Territory herbaria. The data can be selected, displayed and visualized in different ways. The data are retrieved and displayed as is from each herbarium, including data errors and difference in data storage conventions. It is important to note that the data represent the state of specimens in herbaria, some or many of which may not yet have been updated; furthermore, the herbaria do not all identify their collections according the the same botanical treatments. Thus the patterns of the AVH are indicative rather than absolute. The data are constantly tested and improvement in quality and confidence is continual.

The help provided in these pages is designed to assist users in understanding the limitations of the data and and achieve the best from their queries.

Herbarium abbreviations

Throughout the help pages, 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

General

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 either side of the search term, or both, to make the desired pattern.

Plant name

You can query on up to five plant names at a time. Note that different herbaria may not follow the same system of classification, so you may need to query on a synonym in order to retrieve matches from all herbaria. For example, some herbaria continue to recognise the genus Dryandra (rather than placing it under Banksia), so, if you are querying for Banksia armata records, you may wish to include Dryandra armata in the query.

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

• Australian Plant Name Index (APNI)
• Australian Plant Census (APC)
• International Plant Name Index (IPNI)
• Index Fungorum
• Australian Marine Algal Name Index (AMANI)
• Algaebase
• Interactive Catalogue of Australian Fungi (ICAF)
• Checklist of the Lichens of Australia

Australian Plant Census. The Australian Plant Census (APC) is a cooperative project currently being developed by the Council of Heads of Australasian Herbaria (CHAH). The APC will provide a consensus view of the taxa that occur in Australia, an overview of alternative taxonomies and complete lists of synonyms. Once completed, information from the APC will be incorporated into the AVH, giving users the option to view records for nomenclatural synonyms without having to query on multiple names.

Family

Australian herbaria do not all use the same system of plant classification. Because the delimitation of some families differs between classifications, a query on family may return a different subset of genera from each herbarium. The Australian Plant Census will also provide a consensual classification at the family level. Note that the family classification of non-vascular plants is in a state of flux; querying by family for non-vascular plants will not be very reliable.

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 Angiosperms; Dahlgren et al. for monocots; Brummitt for gymnosperms; various for pteridophytes
• Northern Territory Herbarium (DNA): Cronquist for angiosperms; Kubitzki for pteriodphytes and gymnosperms
• Tasmanian Herbarium (HO):
• 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):
• Western Australian Herbarium (PERTH): Cronquist (with modifications) for angiosperms (for more information on PERTH's system see: Paczkowska, G. & Chapman, A.R. The Western Australian flora: a descriptive catalogue, Western Australian Herbarium, Perth, 2000, pp. 8-9)

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

• The Angiosperm Phylogeny Group, 'An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants: APG II', Bot. J. Linn. Soc., 2003, vol. 141, pp. 399-436.
• Singh, G. Plant systematics: an integrated approach, Science Publishers, New Hampshire, 2004.
• Flora of Australia. Vol. 1, Introduction 2nd edition, Australian Biological Resources Study/CSIRO, Melbourne, 1999.
• Brummitt, R.K. Vascular plant familes and genera, Royal Botanic Gardens, Kew, 1992.
• Kubitzki, K. (ed.) The families and genera of vascular plants. Vol. 1, Pteridophytes and gymnosperms, Springer-Verlag, Berlin, 1990.

Qualifiers

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
• ? = questionable
• 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 qualifiers in your query, except for ‘incorrect’.

Note that qualifier data is currently only being provided by the following herbaria: AD, CANB, HO, MEL, PERTH. Records returned from other herbaria may include qualifiers, although they won’t be displayed.

Bulk searching

The Upload file for bulk searching feature allows users to search for more taxa than the search limit provided by the form.

Files can contain genus, species, infrarank and infraname 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. Comma and space delimiters cannot be used together in the one file. Note that infrarank must be one of the following values, and must include the full point:

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

For example:

genus1

genus2, species2

genus3, species3, infrarank, infraname

OR

genus1

genus2 species2

genus3 species3 infrarank infraname

Determination

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

Note that determination information is currently only being provided by the following herbaria: AD, BRI, CANB, NSW, PERTH.

Location

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 others after the event; others have been automatically generated; others are the result of historical interpretation, and others have changed through geopolitical adjustments.

Country

To be added

State

To be added

Botanical region

To be added

Nearest named place

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

Note that Nearest Named Place is currently only being provided by the following herbaria: AD, BRI, CANB, HO, 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, consider entering a search term with a wildcard (%) either side, e.g. '%simpson desert%'

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% 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 being provided by the following herbaria: AD, BRI, CANB, HO,MEL, 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% 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 only being provided by the following herbaria: AD, BRI, CANB, MEL, NSW.

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 10000, will have been collected within a 10 km radius of the geocode assigned to that collection.

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).

Note that geocode source is currently only being provided by the following herbaria: AD, BRI, CANB, HO, MEL, NSW, PERTH.

Range 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 (note that -38 degrees is lower than -36 degrees).

Centroid query

The centroid query allows you to query for records within a specified distance of a given point. You can define a query either as a distance in minutes from a point of latitude and longitude, or as a distance in metres from an Australian Map Grid reference.

Collection

Collector

The name of the primary collector. For a more effective search, consider entering the surname of the collector with a wildcard (%) either side, e.g. '%beauglehole%'.

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, considering entering the surname of the collector with a wildcard (%) either side, e.g. '%bean%'.

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 the possibility of duplicate numbers you should also enter the a herbarium in the previous field.

Note the following prefixes and suffixes apply:

• AD:
• BRI: All BRI accession numbers are prefixed by 'AQ', which must be included in the query.
• CANB: Divided mixed collections have been given suffices 'a', 'b', etc. The recent practice is to append a sequential decimal number.
• DNA:
• 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 appear 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 are unsure whether the collection has multiple components, or if you wish to view all components, use the wildcard character (%).

Cultivated records

To be added

Collection date

To be added

Date range query

To be added

Curation

This page will allow herbarium curators to query on curatorial fields. Record update date is currently available for searching, but other fields are still under development.

Duplicate specimens at

Herbaria to which duplicate specimens have been sent. Institutions are listed by Index Herbariorum code.

Loan job number

The unique insitutional loan number used to identify a loan.

Note that loan job number is currently only being provided by the following herbaria: AD, CANB.

Loan item (specimen) number

The sequence of an individual specimen within a loan. Not all herbaria assign loan item numbers to specimens.

Note that loan item number is currently only being provided by the following herbaria: AD, CANB.

Exchange job number

The unique institutional loan number used to identify a loan.

Note that no herbaria are currently providing exchange job number.

Exchange item number

The unique number assigned to a specimen with an exchange transaction. Not all herbaria assign exchange item numbers to specimens.

Note that no herbaria are currently providing exchange item number.

Donor

The Index Herbariorum code of the institution from which the accessioned specimen was obtained.

Note that donor institution data is currently only being provided by the following herbaria: CANB, NSW.

Donor accession number

The accession number of the institution from which the specimen was obtained.

Note that donor accession number is currently only being provided by the following herbaria: CANB, NSW.

Type

Use this field to search for a particular type status by using one of the values below, or for all types by using the wildcard (%).

Type abbreviations

Abbreviation	Expansion
EPI	epitype
HOLO	holotype
ISO	isotype
ISOLECTO	isolectotype
ISONEO	isoneotype
ISOPARA	isoparatype
ISOPARALECTO	isoparalectotype
ISOSYN	isosyntype
KLEPTO	kleptotype
LECTO	lectotype
NEO	neotype
PARA	paratype
PARALECTO	paralectotype
SYN	syntype
TOPO	topotype
TYPE	unspecified type material

Note that not all herbaria abbreviate type status so you may get more accurate results by including the wildcard after the abbreviation. Include a wildcard before the abbreviation if you want to include uncertain types (which are sometimes prefixed by a question mark) in your query. A search on '%type' will return all categories of types.

Validation level

To be added

Record creation date

The date that the record was created at the source institution.

Note that this data is currently only being provided by the following herbaria: AD, CANB.

Record update date

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

Note that this data is currently only being provided by the following herbaria: AD, CANB, DNA, HO, NSW, PERTH.