Consortium Help & Resources<\/strong> (2026) Workflow for creating advanced checklists using Symbiota tools built into the Consortium of Lichen Herbaria.<\/em> URL https:\/\/help.lichenportal.org\/index.php\/en\/2024\/08\/workflow-for-creating-advanced-checklists\/ [Accessed 25 February 2026].<\/p>\n\n\n\n
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This tutorial describes a detailed workflow using Symbiota tools in the Consortium of Lichen Herbaria<\/em> for compiling checklists based on specimen records available in the Consortium as well as records published in the literature.<\/p>\n\n\n\n For a general tutorial on ho to create checklists in Symbiota refer to the Symbiota Help Documentation on Checklists<\/a>. There is also a beginner’s tutorial available here<\/a>.<\/p>\n\n\n\n An example checklist was recently published for the country of Ecuador: Lichen-forming, Lichenicolous and Allied Fungi of Ecuador<\/a>. An example how to create checklists in SEINet was recently published in Vol. 17 of Canotia<\/a> by by Mackenzie E. Bell and Leslie R. Landrum: Making Checklists with the SEINet Database\/Symbiota Portals<\/a>.<\/p>\n\n\n\n Building checklists and managing checklist data using the Consortium provides an efficient and dynamic option to deal with large species lists from megadiverse countries, especially when dealing with poorly known groups, where the taxonomy frequently changes.<\/p>\n\n\n\n For a more detailed discussion of using the Symbiota tools, please review our publication:<\/p>\n\n\n\n Y\u00e1nez-Ayabaca et al. <\/em>(2023) Towards a dynamic checklist of lichen-forming, lichenicolous and allied fungi of Ecuador<\/a>. The Lichenologist<\/em> 55<\/strong>(5):203-222 [open access].<\/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 Before you get started, it is a good idea to decide which kind of list you are planning to build. <\/p>\n\n\n\n Checklists built with Symbiota can be simple <\/em>or they can be hierarchical<\/em>. Thus, for a large country with many different provinces, it may make sense to build individual checklists for each province first, and then include these as children checklists for the country. The parent checklist will automatically inherit taxa included in any of the child checklists. Thus, you can build a checklist for Mexico, by first creating separate checklists for each state (Baja California, Chihuahua, Sinaloa, etc.) and then add these as children to its parent the national checklist for Mexico.<\/p>\n\n\n\n There are also some disadvantages to be considered when creating hierarchical lists:<\/p>\n\n\n\n (1) Hierarchical lists add complexity \u2013 each change made to any of the children checklists will be reflected in the parent. Managing a version history of checklists (see below) thus becomes more challenging, especially when dealing with a large country with many provinces and thus one principle list with multiple child checklists.<\/p>\n\n\n\n (2) Detailed information entered for a specific taxon may be different for a child checklist vs. its parent. Generally, information from the child checklist also appears in its parent – unless different information is entered there. Only if information has been entered for the parent it then supersedes information entered for the child. <\/p>\n\n\n\n An example: a species might be rare in one state (or province), but common in most of the country. To emphasize this difference, one would have to include a comment that the species is rare in that particular state, but also add a comment to the national checklist that the species is generally quite common throughout most states of the country.<\/p>\n\n\n\n Again this means: for large countries with many states (or provinces) maintaining separate hierarchical checklists adds a level of complexity and thus, higher maintenance of these checklists overall.<\/p>\n\n\n\n It is also possible, to use a mixed approach \u2013 building an general checklists of all species reported from a country, plus a few additional checklists only for the states\/provinces that are best known, the ones having received the most attention. The Checklists of Ecuador as an example for hierarchical checklists: <\/strong> Hierarchical checklists are useful to distinguish lichen biota across geopolitical\/geographic regions. But there are also two additional categories of child checklists:<\/p>\n\n\n\n \u2191 back to the top<\/a><\/p>\n\n\n\n ‘Rare, Threatened & Protected Species Checklist’ <\/strong>\u2012 this category is set up to include species from a region (country, state, etc.) that are considered rare and potentially threatened. Building such a checklist can be used to hide locality data for specimens vouchers from public view. Even though this checklists feeds data into the parent, vouchers included in this list will not be displayed on a map. These occurrence records remain hidden from the public and are accessible only with user rights that allow reviewing rare species occurrences. An example is the ‘Red-List of Endemic Galapagos Lichens<\/a> (however: currently most records in this list are not hidden, because this is a list of draft assessments)’.<\/p>\n\n\n\n and<\/em><\/p>\n\n\n\n ‘Species Exclusion List’<\/strong> \u2012 this category is set up for building checklists of taxa that have erroneously been reported from a region (country, state, etc.); unlike any other child checklist, taxa from an ‘species exclusion list<\/em>‘ will not be included in its parent. An example is the list of ‘Erroneous reports of lichen-forming, lichenicolous and allied fungi from Galapagos<\/a>‘.<\/p>\n\n\n\n _______________________________________________________________________________________<\/p>\n\n\n\n \u2191 back to the top<\/a><\/p>\n\n\n\n Checklists can either be constructed by adding taxa manually<\/em>, in batch<\/em>, or using the Voucher Tool<\/em>. Adding taxa (species, subspecies, varieties, forms) to build a checklist only taxa available <\/em>in the Taxonomic Thesaurus can be added. Taxa not included must first be added to the thesaurus before they can then be added to a Checklist (contact the portal administrator, if a taxon is missing from the thesaurus).<\/p>\n\n\n\n When building checklists manually <\/em>it is strongly recommended to first review whether a name is considered ‘accepted’ or a ‘synonym’. Per default, taxa are being displayed in a checklists how they were originally added to that list, i.e., the ‘original checklist<\/em>‘. <\/p>\n\n\n\n Building a list from scratch it is possible to accidentally add two different names of the same species. By switching the display from ‘Original Checklist’ to ‘Central Thesaurus’ it is possible to review, whether accidentally different names of taxa have been added, which the thesaurus considers synonyms (see Taxonomy Cleaning below).<\/p>\n\n\n\n To manually add species records to your checklist, make sure ‘spp-on<\/strong>‘ is active (this option also needs to be enabled to manually edit any notes for each entry, discussed in detail later):<\/p>\n\n\n\n This opens a box where you can start typing species names to add them manually. For each species you can also additional information (family override, habitat, abundance, notes, internal notes, and source):<\/p>\n\n\n\n When you add individual species records to your checklist manually, it is important not to add duplicates of the same species using different names for the taxon.<\/p>\n\n\n\n For example, it is possible to accidentally add both Usnea longissima<\/em> Ach. and Dolichousnea longissima<\/em> (Ach.) Articus to the same checklist \u2012 even though these are just different names for the exact same<\/em> species, i.e., both taxa are based on the same type (= homotypic synonyms), simply reflecting different taxonomic opinions<\/em> how the species should be named.<\/p>\n\n\n\n It is possible also to add names that the taxonomic thesaurus treats as heterotypic <\/em>synonyms, i.e., taxa that are based on different types, but nevertheless considered synonyms. Taxonomic opinions change over time and authors of a checklist may disagree, thus this provides for an option not to follow the taxonomic concepts employed by the thesaurus. <\/p>\n\n\n\n For example, following the Lichen Flora of the Greater Sonoran Desert Region<\/em>, the taxonomic thesaurus lists Buellia glaziouana<\/em> (Kremp.) M\u00fcll. Arg. as a synonym of Buellia mamillana <\/em>(Tuck.) W.A. Weber. The two taxa are based on a different type and could be considered distinct species (again: this is a matter of opinion). In some instances, authors may deliberately disagree, treating two taxa as separate species, although the thesaurus considers them synonyms.<\/p>\n\n\n\n Changing the display option from ‘Original Checklist’ to ‘Central Thesaurus’ will then result in different statistics,. The ‘Original Checklist’ display will then display and different species count from the ‘Central Thesaurus’. While the ‘Central Thesaurus’ only counts the number of accepted names, the ‘Original Checklist’ counts all names that have been originally added to the list separately \u2012 no matter whether these are synonyms or not. <\/p>\n\n\n\n Therefore, when adding synonyms as separate species not<\/em> following theCentral Thesaurus, it is recommended to add a comment explaining the different taxonomic opinion. In most instances discrepancies arise, however, not because authors deliberately decided to disagree with the Central Thesaurus, but when false duplicates have been added accidentally. Then, it is necessary to download, compare and clean up the two lists [see Taxonomy Cleaning below].<\/p>\n\n\n\n \u2191 back to the top<\/a><\/p>\n\n\n\n Instead of adding individual species manually one-by-one, it is possible also to upload an entire spreadsheet (= a list of species) in batch.<\/p>\n\n\n\n That spreadsheet may include only a single column, a simple list of the names to be added, or it can be a spreadsheet with one or several of the following fields:<\/p>\n\n\n\n sciname | family override | habitat | abundance | notes | internal notes | source<\/strong><\/p>\n\n\n\n The only acceptable file format that can be uploaded is a text file with comma separated values<\/em> [file extension: *.csv]. To manually compile such a file, you could use a text editor and separate columns by comma and enclose text that itself contains commas in quotation marks. However, most spreadsheet programs [e.g., Excel, LibreOffice CALC] allow you to save files directly as CSV. To assure that symbols are transcribed correctly, is recommended to save the CSV with UTF-8 encoding. <\/p>\n\n\n\n Below the list of fields that can be uploaded in batch [with the size and whether their title is displayed]:<\/p>\n\n\n\n sciname <\/strong>= The sciname <\/em>is the ‘scientific name’ of a species without its author<\/em>. Although a spreadsheet may include author names, during upload these are nevertheless ignored. The consequence: homonyms will not be distinguished during upload. So, if you upload a name like Caloplaca arizonica <\/em>E.D. Rudolph [= a synomym of Caloplaca pellodella<\/em> (Nyl.) Hasse] vs. Caloplaca arizonica<\/em> H. Magn. [= a synomym of Gyalolechia epiphyta<\/em> (Lynge) Vondr\u00e1k] the two are not distinguished during upload. If you have a good reason, why homonyms must be added to a checklist, it is recommended to add them manually. An example are homonyms, where a replacement name has not yet been published. Thus, the name Herpothallon hyposticticum<\/em> was published twice \u2012 once as a species assumed to be endemic to the Galapagos, then also for a species reported from Florida. The name that was published first, Herpothallon hyposticticum<\/em> Bungartz & Elix from the Galapagos, has taxonomic priority. The name introduced for the species in Florida Herpothallon hyposticticum<\/em> F. Seavey & J. Seavey is thus illegitimate. But as long as no replacement name has been published for the species from Florida, that taxon is still listed in the North American Checklist<\/a>.<\/p>\n\n\n\n family override<\/strong> [max. 50 characters, title not <\/em>displayed] = This field is not being displayed, but it can be used to organize a checklist using family names different from the Central Thesaurus. Thus, you may not accept the separation of Physciaceae <\/em>and Caliciaceae<\/em>, but prefer to treat both as subfamilies of one and the same superfamily. Or you may consider that the genus Ramalina <\/em>should be listed in Ramalinaceae<\/em>, not Bacidiaceae<\/em>. This is possible by adding the preferred family name here, one that differs from the Central Thesaurus.<\/p>\n\n\n\n habitat <\/strong>[max. 500 characters, title not <\/em>displayed] = This field was originally intended to display information about the habitat where a species is known to occur. For species included in checklists built for the Lichen Consortium the habitat field is sufficiently large to include the Esslinger categories whether a taxon is lichenized, a lichenicolous fungus, or a saprophytic or allied fungus [see ‘Assign Categories<\/a>‘ below].<\/p>\n\n\n\n Some records of lichenicolous fungi included in the Ecuador Checklist:<\/strong> abundance <\/strong>[max. 50 characters, title not <\/em>displayed] = This field is relatively small. For the Galapagos Checklist we have used this field to distinguish whether a taxon is considered endemic, native and\/or indigenous to the archipelago [see ‘Assign Categories<\/a>‘].<\/p>\n\n\n\n notes <\/strong>[max. 2,000 characters, title not <\/em>displayed] = The notes field is sufficiently large to add detailed comments about a taxon, for example, if a taxon is considered problematic and why (it might have been only reported in the literature many years ago and no modern records exist, or the correct identification of specimens on which the report is based remains doubtful, etc.) [see ‘Assign Categories<\/a>‘].<\/p>\n\n\n\n Screenshot from the Ecuador Checklist:<\/strong> internal notes<\/strong> [max. 250 characters, this field is not <\/em>displayed at all] = The field is not displayed and intended for comments that only checklist editors have access to. It is generally not very useful, because it is ‘invisible’ even to editors unless the data entry from is opened for each single taxon (or the whole checklist is downloaded as a spreadsheet). source <\/strong>[max. 1,100 characters, title displayed as ‘source<\/span>:’] = The source field is intended for literature citations. Although the field is quite large, it is not sufficient to add full reference citations here. A workaround is to use the general format how publications are typically cited in the scientific literature [e.g., Cole & Hawksworth (2001) or Suija et al. (2015)] and maintain a separate document with the full reference list, later to be added for download as a PDF, once the final list is being published [see the Ecuador Checklist<\/a> as an example].<\/p>\n\n\n\n \u2191 back to the top<\/a><\/p>\n\n\n\n Here an example of a CSV file with records in the format ready to be uploaded (a CSV file with UTF-8 character encoding):<\/p>\n\n\n\n Download the file, create a new, empty checklist and upload the data in batch:<\/p>\n\n\n\n This file will create a checklist providing some examples with the formatting, comments and colored categories used in the Ecuador Checklist (make sure to configure the display options to show the synonyms, notes & vouchers, taxon authors and organize the checklist alphabetically by genus, not family):<\/p>\n\n\n\n \u2191 back to the top<\/a><\/p>\n\n\n\n The previous CSV file is a clean <\/em>data set using the current taxonomy of the Central Thesaurus. Here a test file that that contains several problematic taxon names:<\/p>\n\n\n\n This file includes only two columns: sciname <\/em>| source<\/em>.<\/p>\n\n\n\n For the exercise, create a new checklist and upload the data from this CSV in batch. Here the result:<\/p>\n\n\n\n During upload, the authors were ignored. Nine taxon names could not be matched against the taxonomy of the Central Thesaurus. For example, line 477 of the CSV simply contains just an ‘x’ instead of a scientific name. That, of course, is not a name and the ‘x’ is thus ignored.<\/p>\n\n\n\n But eight other names could also not be matched. These names is erroneous:<\/p>\n\n\n\nTable Of Contents<\/h2>\n\n\n\n
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1. ‘Hierarchical’ vs. ‘Non-Hierarchical’ Checklists<\/h2>\n\n\n\n
Geographic\/Geopolitical Hierarchies<\/strong><\/h3>\n\n\n\n
Thus, in Mexico, for example, the northwestern states of Sonora, Baja California, and Baja California Sur have been reasonably well investigated as a result of the Lichen Inventory for the Sonoran Region<\/em>, whereas only few species records are known from some of the other states in Mexico.<\/p>\n\n\n\n![\"\"](\"https:\/\/help.lichenportal.org\/wp-content\/uploads\/2024\/08\/image.png\")
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Four lists are available – (1) the main list for the Country of Ecuador<\/em>, (2) a list for the Province of Galapagos<\/em>, (3) a Red-List with draft assessments<\/em> of species endemic to the Galapagos, and (4) a list of species erroneously reported from the Galapagos.
The main list of the country is configured as the parent of the Galapagos Checklist<\/em>. The Galapagos Red-List<\/em> is a child of the Galapagos Checklist <\/em>and it is configured as a ‘rare, threatened and protected species list<\/em>‘ [see below]. The list of Species erroneously reported from the Galapagos<\/em> is a ‘species exclusion list<\/em>‘, thus not feeding its records into the parent [also see below].<\/p>\n\n\n\n2. Upload Existing Lists<\/h2>\n\n\n\n
2.1. manually adding taxa<\/h3>\n\n\n\n
![\"\"](\"https:\/\/help.lichenportal.org\/wp-content\/uploads\/2024\/08\/image-1-1024x189.png\")
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<\/figure>\n\n\n\n2.2. uploading checklists in batch<\/h3>\n\n\n\n
![\"\"](\"https:\/\/help.lichenportal.org\/wp-content\/uploads\/2024\/08\/image-10-1024x641.png\")
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The Esslinger category ‘lichenicolous’ has been added in color using html tags [see ‘Assign Categories<\/a>‘], and the genus or species from which the lichenicolous fungus has been reported has been entered into the habitat field as well.
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For Acantholichen galapagoensis<\/em> the ‘abundance’ field contains the comment ‘endemic to Galapagos’, the ‘notes’ include a reference to the holotype and a comment that the species has been red-listed by the IUCN as vulnerable, as well as a comment that the species was previously erroneously reported from the Galapagos as A. pannarioides<\/em>. The ‘source’ field lists relevant literature for which the complete list of references is included in a PDF that can be downloaded from the website. [different colors can be used with html tags, see ‘Assign Categories<\/a>‘].<\/p>\n\n\n\n
Collaborating on a checklist draft, it is generally more convenient to temporarily use the other fields for adding ‘working notes’ (perhaps tagging them with a different color) and deleting them before publication, once the issue has been resolved.<\/p>\n\n\n\n![\"\"](\"https:\/\/help.lichenportal.org\/wp-content\/uploads\/2024\/08\/image-6-1024x321.png\")
<\/figure>\n\n\n\nexercise #1:<\/strong><\/h3>\n\n\n\n
![\"\"](\"https:\/\/help.lichenportal.org\/wp-content\/uploads\/2024\/08\/image-20.png\")
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<\/figure>\n\n\n\nexercise #2:<\/strong><\/h3>\n\n\n\n
![\"\"](\"https:\/\/help.lichenportal.org\/wp-content\/uploads\/2024\/08\/image-23-1024x941.png\")
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