In this Workflow Tutorial we provide general recommendations on best practices for data management for specimens of lichenized, lichenicolous and allied fungi<\/strong>:<\/p>\n\n\n\n collecting<\/a> \u2192 curating<\/a> \u2192 managing specimen data<\/a> \u2192 imaging specimens \u2192 routine microscopy \u2192 thin-layer chromatography<\/a> \u2192 DNA-extraction & barcoding<\/p>\n\n\n\n _______________________________________________________________________________________<\/p>\n\n\n\n _______________________________________________________________________________________<\/p>\n\n\n\n \u2191 back to the top<\/a><\/p>\n\n\n\n Managing specimen records in a professional database has many advantages. To this day, large historic collections are typically still not fully databased. Many smaller collections and private researchers with only limited resources often use simple spreadsheets or custom-made databases to keep track of their collections.<\/p>\n\n\n\n This is not a good idea…<\/em><\/p>\n\n\n\n Spreadsheets typically do not follow any established standards, how collection data should be organized, which information should be recorded when collecting specimens, and how that information should be stored. Spreadsheets are designed to execute mathematical calculations, sorting rows and columns can inadvertently mix up records and corrupt the data.<\/p>\n\n\n\n A simple spreadsheet cannot keep track of relational data. For example, it is not possible to store a history of how specimen identifications have changed over time. It is not possible to link several different images, genetic or molecular records to the same specimen either. In a flat file, with rows and columns these kind of relationships cannot be established.<\/p>\n\n\n\n Software to build relational database also has disadvantages. Custom built relational databases often also do not adhere to biodiversity data standards and thus data typically cannot easily be exchanged.<\/p>\n\n\n\n The main purpose of databaseing specimen records is not just to keep track of a collection, but to share information, making specimen records accessibly to a broader community of researchers and collaborators. <\/p>\n\n\n\n This is particularly important for type specimens, i.e., the physical “gathering of specimens” that are required to be deposited in a collection when new species are being described. The reason, why the Code of Nomenclature<\/a> requires that scientific names must based on types , is simple:<\/p>\n\n\n\n A species name represents a hypothesis (i.e., that this name refers to a particular species distinct from all others, but also more closely related to some). To be scientifically sound, it must be possible to test these hypotheses by reviewing the material a name is based upon. Types must therefore be accessible for research.<\/p>\n\n\n\n But other specimens are also valuable only, if they are accessible, if they can be studied, examined, compared. Researchers thus benefit from unhindered access to collections – both the ones who originally collected the material (and their institutions), as well as other who get the opportunity to study the material.<\/p>\n\n\n\n No specimen determination, no identification, no name is final. The idea that data must not be shared, that specimen records must only be made available, when the material has “accurately been identified”, is absurd. How can it be justified to collect living organisms during a biodiversity crisis, with many species threatened, if we not at least use these collections to share and advance knowledge?<\/p>\n\n\n\n As the legacy of colonialism, many historic collections throughout Latin America, Africa, and Asia are today hosted mostly in European and often also North American collections. Researchers from these parts of the world are as a result often reluctant to share records or more recent collections widely. This, ironically, is today one of many impediments to advancing global biodiversity knowledge. Fortunately, most countries today have agree to share their data through the Global Biodiversity Information Facility<\/a> (GBIF). <\/p>\n\n\n\n At a very minimum, to facilitate data sharing, Biodiversity Data Standards proposed by the Taxonomic Database Working Group (TDWG) should be followed, when managing specimen records – even if only in spreadsheets.<\/p>\n\n\n\n The Consortium of Lichen Herbaria<\/a> offers an option to share specimen records directly with the global community of researchers working on lichenized, lichenicolous, and allied fungi. <\/p>\n\n\n\n Records can be managed live, directly online, without the need to install software, purchase or invest resources to build a customized database. The Consortium database is fully compliant with the DarwinCore, which means that records can easily be configured to automatically be shared with GBIF; records in GBIF can thus also be updated, when they are modified in the Consortium.<\/p>\n\n\n\n Tools built into the Consortium include a regularly updated Taxonomic Thesaurus (handling accepted names vs. synonyms), a Taxonomic Name Cleaner that facilitates fixing erroneous taxon names, the option to keep track of name changes when specimens are reviewed and annotated by a researcher, tools to link GenBank sequence data and images of specimens, options to track and manage loans, print labels and annotation slips, batch harvest ecological traits from specimen data, and much more.<\/p>\n\n\n\n Managing data live <\/em>in the Consortium has the benefit of records always being up-to-date. However, it is possible also to share snapshots, i.e., data sets being managed locally and regularly being updates. Having invested in their local, in-house data software, large collections often prefer this option, when sharing their data through the Consortium.<\/p>\n\n\n\n Whether managing data locally in a spreadsheet (not recommended), in a standalone local database (sharing it as a snapshot), or managing records live online in the Consortium, closely adhering to Biodiversity Data Standards is necessary for sharing the data:<\/p>\n\n\n\n _______________________________________________________________________________________<\/p>\n\n\n\n \u2191 back to the top<\/a><\/p>\n\n\n\n Symbiota, the open-source software platform used by the Consortium of Lichen Herbaria is DarwinCore compliant<\/em>, which means that, with very few exceptions, it adheres to Biodiversity Data Standards proposed by the Taxonomic Database Working Group (TDWG).<\/p>\n\n\n\n Symbiota supports some fields (such as ‘substrate’) that are not currently supported by the DarwinCore. Some field names used by the Symbiota databases are for convenience occasionally named differently from the terminology employed by the DarwinCore. Thus, the DarwinCore term ‘recordedBy’ is typically the ‘collector’ or ‘observer’ of a record.<\/p>\n\n\n\n During database backups, or when exporting or importing records, or when uploading collections to the Global Biodiversity Information Facility (GBIF), the data set format uses the terminology employed by the DarwinCore and any additional fields are merged (for example: ‘substrate’ is added to ‘habitat’) to assure complete full compatibility for exchanging biodiversity data sets.<\/p>\n\n\n\n _______________________________________________________________________________________<\/p>\n\n\n\n \u2191 back to the top<\/a><\/p>\n\n\n\n The Occurrence Editor in Symbiota provide a short dictionary with explanations of the field names and links to the DarwinCore terms:<\/p>\n\n\n\n Below, we provide recommendations and examples<\/strong> when dealing with data management of records for lichens, lichenicolous and allied fungi<\/strong>:<\/p>\n\n\n\n _______________________________________________________________________________________<\/p>\n\n\n\n \u2191 back to the top<\/a><\/p>\n\n\n\n \u2191 back to the top<\/a><\/p>\n\n\n\n Catalog Numbers are unique identifiers for a specimen record<\/strong>; to avoid data entry mistakes it is recommended to use barcodes with a hand-held barcode scanner during data entry. Catalog Numbers are typically assigned when a specimen is accessioned into a collection. Thus they are often also called Accession Numbers.<\/p>\n\n\n\n Recommendation: <\/strong>Choosing a barcode format it is best to include the collection acronym, but avoid special characters or symbols, for example ASUL019347 rather than ASUL-019347. Resources:<\/strong> LichenLabler<\/a> is a small program that you can download to print your Catalog Numbers as barcodes directly onto a packet.<\/p>\n\n\n\n Specimen barcode stickers:<\/strong> Code 128 allows for very small barcodes; at ASU we use six digit codes with the prefix ASUL, each sticker 0.875 \u00d7 0.412 inch (= 22 \u00d7 10 mm) on rolls of 1,000.<\/p>\n\n\n\n _______________________________________________________________________________________<\/p>\n\n\n\n \u2191 back to the top<\/a><\/p>\n\n\n\n Additional Identifiers<\/strong> are useful to preserve any legacy numbers that at some point in the history of a specimen served as its identifier.<\/p>\n\n\n\n Some Examples: <\/strong><\/p>\n\n\n\n (1) A specimen has been donated as a gift from a different collection. If that specimen was originally assigned a Catalog Number from the donor institution, this original catalog number should be stored as an additional identifier. <\/p>\n\n\n\n (2) Collectors decide re-assign different numbers, switching for example from one numbering format to a different one. In this case the original number should be preserved as additional identifier. <\/p>\n\n\n\n (3) Catalog Numbers may also change and the legacy numbers (or Other Catalog Numbers) should then be stored as additional identifiers (e.g., ASU migrated from a six digit number barcodes to ones that include ASUL as a prefix). <\/p>\n\n\n\n (4) Original Catalog Numbers need to change when two collections merge and one collection is being integrated into another one. UCR donated all its liken collections to SBBG; the additional identifiers can be used to preserve the UCR catalog numbers while assigning new SBBG numbers. It has been announced that all collections at DUKE will be integrated into UNC. The legacy catalog numbers from DUKE must be preserved as additional identifiers.<\/p>\n\n\n\n (5) Often specimens are collected as part of a specific project, an inventory or ecological study. If researchers assign identifiers as part of this project, these numbers should be preserved when the specimen is eventually accessioned into the collection and then assigned a unique Catalog Number.<\/p>\n\n\n\n (6) The United States National Park Service maintains a database of specimens that reside under permanent loan agreements in different collections. To match catalog numbers from the Park Service database to a Catalog Number assigned by the collection where the specimen is stored, additional identifiers should be used.<\/p>\n\n\n\n Additional Identifiers are a combination of the original numbers (or “values”) that were at some point used to identify a specimen with the “tags” that explain what these values mean:<\/p>\n\n\n\n _______________________________________________________________________________________<\/p>\n\n\n\n \u2191 back to the top<\/a><\/p>\n\n\n\n The name of the person who collected a specimen or recorded an observation. <\/p>\n\n\n\n Recommendation: <\/strong>In most cases, lichens cannot reliably be identified in the field, but it is necessary to study anatomical, chemical, or even molecular characters – especially in regions that have poorly been studied. Therefore, it is generally not recommended to only record an observation. Increasingly, researchers can be identified by their Open Researcher and Contributor ID (ORCID number), which may be appended.<\/p>\n\n\n\n Examples:<\/strong> <\/p>\n\n\n\n \u2191 back to the top<\/a><\/p>\n\n\n\n Not to be confused with Field Number<\/a> or Location ID<\/a> or an Exsiccati Number<\/a>.<\/p>\n\n\n\n For the purpose of naming species<\/em>, when selecting nomenclatural types<\/em>, the International Code of Nomenclature for Algae, Fungi and Plants<\/a> distinguishes between “gatherings” and “specimens”. Several specimens that were all collected at the exact same location, on the same day, by the same researcher belong to a single gathering. <\/p>\n\n\n\n When describing a new species, the Code of Nomenclature requires that specimens selected as types <\/em>must belong to the same gathering, i.e., found during a single collecting event and assigned the same collecting number<\/strong><\/em>. It is generally assumed that holotypes (= the original specimen, typically deposited at the researchers home institution) and isotypes (= duplicates distributed elsewhere) bear the same number.<\/p>\n\n\n\n Another name commonly used for this number is collection number<\/em>, or perhaps more accurately called collector number<\/em>, because the number is typically assigned by the collector of the specimen.<\/p>\n\n\n\n DarwinCore calls it the recordNumber <\/em>to emphasize that a number may be assigned when a species was only observed, perhaps documented by a photo, but no physical specimen was collected.<\/p>\n\n\n\n Recommendation:<\/strong> A variety of formats is often used by researchers. Best practice is to assign collector numbers not in the field, but in the lab during specimen processing. For simplicity it is best to use sequence numbers. It is recommended to assign the same number to a specimen and append it by letters, if different species on the same substrate cannot physically be separated (e.g., different species on the same rock, lichenicolous fungi on a host lichen). Duplicates of specimens collected as part of the same gathering, to be distributed to other collections, should not be assigned different numbers.<\/p>\n\n\n\n <\/p>\n\n\n\n \u2191 back to the top<\/a><\/p>\n\n\n\n This field is not defined by the DarwinCore, but it is strongly recommended to distinguish the main collector from any other researchers who joined the same collecting event. When designating type specimens, only the combination of ‘collector+collector number’ uniquely identifies a specimen from the same gathering; therefore several collectors must not share the same ‘collecting number’.<\/p>\n\n\n\n ______________________________________________________________________________________<\/p>\n\n\n\n \u2191 back to the top<\/a><\/p>\n\n\n\n The date when a specimen was collected (= the date of the collecting event).<\/p>\n\n\n\n Recommendation: <\/strong>To avoid confusion dates should be stored according to the ISO-8601 numeric format (YYYY-MM-DD). Unknown month or days may be entered as “00”. For example, a collection with a date of “March 1956” can be entered as “1956-03-00”. However, see also Verbatim Date<\/a>.<\/p>\n\n\n\n Examples:<\/strong> <\/p>\n\n\n\n For some organisms it may not be possible to record an exact date when a specimen was collected (for example insects caught during several days in a pit-fall trap). <\/p>\n\n\n\n Recommendation: <\/strong>For lichens recording the start and end date of a collecting trip is not recommended; instead the exact day when a specimen was collected should be documented; this is implied by entering only a start, but no end date.<\/p>\n\n\n\n <\/p>\n\n\n\n When the exact day of a collecting event has not been recorded or is unknown this text field allows for documentation of the date given on a label. The Verbatim Date field is especially useful for data entry of historic specimens, where an exact date is often not available.<\/p>\n\n\n\n _______________________________________________________________________________________<\/p>\n\n\n\n \u2191 back to the top<\/a><\/p>\n\n\n\n Exsiccata are a set of dried specimens, numerous duplicates of the same species, all collected at the same locality and identified by the same researcher(s), then distributed to many different herbaria. When these specimens are distributed, a printed list, the so-called ‘schedae’, is published and sent along. <\/p>\n\n\n\n The purpose of these special collections is to distribute, disseminate and thus document a particular species concept. Exsiccata may be types, if they are designated as such. However, most exsiccata simply document the taxonomic opinion of a particular researcher, what constitutes a particular species. <\/p>\n\n\n\n Recommendation:<\/strong> Due to their unique importance, exsiccata should, like types, be stored separately from the main collection. The Consortium includes an Index of Exsiccatae<\/a>, from which titles must be selected when entering specimens. These titles can also be found at IndExs<\/a>.<\/p>\n\n\n\n <\/p>\n\n\n\n The Exsiccata Number is the number under which an exsiccatum, i.e., one particular specimen in the set of species called exsiccata, was published. This number is listed on the label typically in front of the species name under which the exsiccatum was distributed; it is also the sequence number in the list that was published as schedae, when the exsiccata was distributed.<\/p>\n\n\n\n NOTE:<\/strong> The correct name for a set of dried plant <\/em>specimens is ‘exsiccata<\/em>‘, in the case of fungi ‘exciccati<\/em>‘. A single specimen, not the entire set, is called ‘exsiccatum<\/em>‘.<\/p>\n\n\n\n _______________________________________________________________________________________<\/p>\n\n\n\n \u2191 back to the top<\/a><\/p>\n\n\n\n Before specimens are accessioned into a collection they are typically identified. Typically the first identification is not yet the final one. For example, it may only be possible to assign the material to a particular family or genus, but not yet a species. Names also change for taxonomic reasons (e.g., when a species is transferred into a different genus). Often expert also disagree on the correct identification. <\/p>\n\n\n\n Professional specimen management systems like the Consortium keep a determination history of how species identifications change. They also typically include a Taxonomic Thesaurus<\/a> that links synonyms to their currently accepted names.<\/p>\n\n\n\n Since January 1, 2013 it is mandatory that scientific names of fungi must be registered in one of the three available international taxonomic names repositories: Index Fungorum<\/a> (Kew, United Kingdom), Mycobank<\/a> (Utrecht, The Netherlands), or Fungal Names<\/a> (Beijing, China). These fungal names repositories use numerical identifiers that are globally unique and synchronized across the three databases [for example Buellia spuria<\/em> (Schaer.) Anzi is identified by Index Fungorum Registration Identifier 380715<\/a> = MycoBank #380715<\/a> = Fungal Names Registration Identifier 380715<\/a>]. <\/p>\n\n\n\n It is not yet universally implemented, but strongly recommended that specimen databases use these identifiers to uniquely identify taxon names.<\/p>\n\n\n\nTable of Contents<\/h2>\n\n\n\n
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General Considerations<\/h2>\n\n\n\n
Databases vs. Spreadsheets<\/h3>\n\n\n\n
Sharing Information: advancing biodiversity knowledge through collaboration<\/h3>\n\n\n\n
Historic Legacy vs. Opportunities for Knowledge Transfer<\/h3>\n\n\n\n
The Consortium of Lichen Herbaria: Biodiversity Data Standards<\/h3>\n\n\n\n
Symbiota & the DarwinCore<\/h2>\n\n\n\n
Field Names, Formatting & Data Entry Recommendations with Examples<\/h2>\n\n\n\n
![\"\"](\"https:\/\/help.lichenportal.org\/wp-content\/uploads\/2026\/09\/image-2-1024x262.png\")
<\/figure>\n\n\n\nCollector Information<\/h2>\n\n\n\n
![\"\"](\"https:\/\/help.lichenportal.org\/wp-content\/uploads\/2026\/09\/7E03E4B3-515A-43F5-B00E-490AEEAFEFE0-1024x372.png\")
<\/figure>\n\n\n\nCatalog Number<\/strong> [dwc:catalogNumber<\/a>]<\/h3>\n\n\n\n
Barcode scanners read barcodes according to the local language settings of a PC. Internationally different keyboards use different layouts. Thus, on an US American keyboard the hyphen \u201c-\u201d is located where on a German keyboard the letter \u00df is placed. If used with a German keyboard ASUL-019347 will thus be transcribed as ASUL\u00df019347.<\/p>\n\n\n\n![\"\"](\"https:\/\/help.lichenportal.org\/wp-content\/uploads\/2025\/07\/image-18.png\")
<\/figure>\n\n\n\nAdditional Identifier Values & Tag Names [Symbiota Field: Catalog Numbers documentation page<\/a>]<\/h3>\n\n\n\n
![\"\"](\"https:\/\/help.lichenportal.org\/wp-content\/uploads\/2026\/09\/image-4.png\")
<\/figure>\n\n\n\nCollector \/ Observer [dwc:recordedBy<\/a>]<\/h3>\n\n\n\n
C.G. Pringle<\/code> Goodding, L.N.<\/code> John Wesley Powell<\/code> M. Andrew Johnston (ORCID 0000-0002-0166-6985)<\/code><\/p>\n\n\n\nCollector \/ Observer Number [dwc:recordNumber<\/a>]<\/h3>\n\n\n\n
Associated Collectors [n\/a – concatenated into dwc:recordedBy<\/a>]<\/h3>\n\n\n\n
Collection Dates<\/h3>\n\n\n\n
Date (start) [dwc:eventDate<\/a>]<\/h3>\n\n\n\n
1983-09-15<\/code> | 1983-07-00 |<\/code> 1934-00-00<\/code><\/p>\n\n\n\nEnd Date [dwc:eventDate<\/a>]<\/h3>\n\n\n\n
Verbatim Date [dwc:verbatimEventDate<\/a>]<\/h3>\n\n\n\n
Exsiccatae<\/h3>\n\n\n\n
Exsiccata Title [n\/a]<\/h3>\n\n\n\n
Exsiccata Number [n\/a]<\/h3>\n\n\n\n
Identification & Determination History<\/h2>\n\n\n\n
![\"\"](\"https:\/\/help.lichenportal.org\/wp-content\/uploads\/2026\/09\/D0E53C5A-2AB1-40FB-8270-10FFBF260669-1024x359.png\")
<\/figure>\n\n\n\nScientific Name [dwc:scientificName<\/a>]<\/h3>\n\n\n\n