BioLists.com

Link 6.   NOTES:  terms used in this series of Sample BioLists

*1   BioLists' CODING CONVENTIONS

      --  Four-digit BDV-#s numbers represent ORDERS.
      --  BioLists uses levels:  ORDER,  Family,  Genus & species (+ 3 categories of Common Names).

      When a BioList is downloaded, its BDV-#s expand to cover the four taxonomic levels - ORDER; Family, Genus, species. eg 2750-3-1-1 could be the listing for a species that is alone (or the first) in the first (or solo) Genus in the third Family for ORDER-2750 = RANUNCULACEAE. (In these notes, unless noted otherwise, all names are from the current Y-v 2000 Classification.)
  
      When a contracted Higher Classification is used, eg "3298-POA-Gra", as in the Ecologic File Format, the three terms represent ORDER-# (3298), ORDER Name (POALES) and Family (Gramineae).

      Higher Classification levels (including Phylum and Class) are named during searches for species' names.

      Note: ORDER Names and BDV-#s cannot be changed within the BioLists program. This guarantees the integrity of the system for and between users. Updating the taxonomy in the BioLists database to follow taxonomic changes will occur between one Year-version and the next. After downloading a BioList, any item can be changed, but users will usually aim to retain the full predictability of the System by not changing BDV-#s.

      Scientific Classification uses a simple convention to show what scientists understand are the evolutionary relationships between species: a one-dimensional coded sequencing strategy is used to list the names. Species thought to be closely related are put close together. Following Darwin and Wallace, the Linnaean convention does this (but alphabetic sequencing is used in the absence of evolutionary sequencing information), so it allows this system to work for what is typically a complex radiation of species rather than a straight-forward progression. Even so, research keeps finding new ideas about relationships, so, as a result of this, taxonomic lists keep changing their sequences - unpredictably. Research taxonomists inevitably cause changes to classifications; it's their job. Their success produces upsets in the use of taxonomic nomenclature, not least because all validly published taxonomic names stay in consideration - for ever!. After experts publish a new classification, they are liable to do more research, and produce more changes.This is how science has coped for two centuries: it can be seen as a monumental muddle, best left to the experts responsible. But the Linnaean Classification System can also be seen as one of the greatest achievements and most powerful assets that Civilisation has produced - if it can be used effectively.

      Changes to Classificatons usually come a few at a time, but occasionally a big new idea strikes and taxonomy undergoes a slow revolution to accommodate it. Following the use of DNA-analysis, we are coping, rather badly, with a massive reorganisation of the Linnaean System; many biologists want to quit and find a "better" system. Some alternative systems have been trialled, but no transitional formats have been produced. Should we stop having organised Classifications of Biodiversity as the sixth Mass Extinction Event (MEE) gains momentum? So far, computers have not helped significantly beyond circulating ever larger, but still limited, selections of names in many wonderful formats. BioLists is different.

*2.  Species Names (Binomial Names: also Scientific or Latin Names, and trivial names, aka species epithets). 
     
     What happens when someone finds a new species? Eventually a description, along with a species name for it is posted in a scientific publication. The description and name are the opinion of the paper's author, one expert, professional or amateur. The "opinion" answers: what has been found to be the new species' closest relatives, and why. Its close relatives will probably be in an existing Genus, so the new species will be given a new "trivial" name - the "species epithet". The combination of "Genus + trivial" names become the new "species name". This double-barreled name is called it's 'binomial' name - a "binomen" (binomena (plural)).

     In print, Genus names and binomena should be italicised or otherwise be in a distinct font from the general text. Names of Genera should always have a Capital letter; never so with "trivial' names. Instead of repeating a Genus name (especially within one paragraph) after the first use the remaining uses of the Genus name are cut to the initial capital letter - Leo tigris becomes L. tigris.

     Many species have been given more than one trivial name in one or more Genera. The "accepted" binomen is the "valid" name, but, despite a basic Law of Taxonomy being to preserve all possible names stability, names often need changing for a wide variety of reasons. "Alternative" names are called "synonyms"; but which is the "right" one? Experts offer opinions, with reasons, in publications. By design, BioList users are spared any need to worry about synonyms. Synonyms can be added to the BioList database and will be made available in due course for advanced and retrospective searching.

      Every species in BioLists Year-version 2000 (Y-v 2000) has a single Species Name (binomen); this is also called its Scientific or Latin Name. Where choice is available with different experts using different names for the same species, BioLists chooses one: this choice is not critical, but taxonomic stability is. The basic aim of BioLists is to help users to share biodiversity information without taxonomic problems complicating the picture or invalidating the data for now or into the future. This stability is important since most biodiversity data can not be recollected - time (and climate change) is always making changes. Standardising scientific names to a BioLists' Year-version list (Classification) does that. But feel free to edit or add any non-standard names for reasons such as using the taxonomy from a favourite text. Using BioLists' standard names will keep datasets compatible; if this is important for keeping your records consistent with others, then don't change any names.

     BioLists does not "support" its non-critical use of species names. Scientific publication requires "authorities" (= publications) to be identified in support of species names. In contrast, BioLists offers users "suggested" names, and it is up to users to ensure that they are using the names they want. If some research work relies on the taxonomy in a particular BioList Year-version, then in writing up the project for publication, the authors will need to refer to authorities, possibly with changes of species names. By deferring all taxonomic problems to the writing up phase, BioList will likely have speeded up the research.

     When you have use for names that are more up-to-date than Y-v 2000, create Y-v 2010 BioLists to access the 2010 database.

     To see the Higher Classification for any species, use the "WORKING" search page for any name; otherwise, ORDER and Family names accompany every record in every BioList.

*3.  UTILITY and TAG Names.

     BioLists is trialling two new forms of species-level COMMON NAMES. Currently, the aim is to see who might find them useful. Please give us feedback. These names are intended to offer new ways of gaining taxonomic stability, convenience and usefulness.

     Every species in the BioLists system is given a unique, formal, contrived, Genus-based UTILITY Name - format: "Genus_a", "Genus_ab", etc. These are specific to a single Y-v (see 6. below).

     Every species also gets a unique TAG Name: where possible, each is a well-known Vernacular Name from the region and language where its species is best known or known to most people. Again, nothing is critical. Until a TAG name is chosen for a species, use the UTILITY name (and there always is one!). Similarly, but optionally, UTILITY or TAG Names may be used where a Vernacular name is not available in any Language, or wherever Vernacular names are not unique.

     By design, UTILITY and TAG names, as such, are not directly searchable, but the names will be found elsewhere (in Genus and/or Vernacular lists).

     UTILITY and TAG Names are "Common Names"; so too, loosely speaking, are VERNACULAR Names such that "Common Names" covers all non-Scientific Names.  

4.  VERNACULAR NAMES.

     Strictly speaking, these are ones in use in a spoken language. When you are specifying a new BioList, you may select one or two Languages. Vernacular Names in the database for the species you select will then be returned along with all their Scientific Names.
     Note that Languages are linked to geographic regions so as to cater separately for regional Floras and Faunas - eg British Isles English caters for a different species mix from New Zealand English.

     Also note that by selecting any two different languages, the Vernacular Names returned effectively translate from one language to the other for any species - for example, between te Reo Maori and New Zealand English.
     Duplications occur with Vernacular names: these can be trimmed from BioLists before or after downloading. Likewise, new Vernacular names can be keyed in at any time; avoid doing this with Utility and Tag Names.

     BioLists wants users to send us names in hundreds of Vernacular Languages. To get your language names and species included, create a Y-v 2000 BioList and ask for it to include your language (or select a related one and tell us the proper name for your one). For Vernacular Names, we are concentrating first on Flowering Plants and then Birds where all Genus Names are already available in the database. Call these up and start adding species names and as many Vernacular names for you language as you can for each species. Most helpful, for BioLists to process these quickly into its database, is for you to list all species in one Genus or one Family at a time.

5.  TAXONOMY --  NAMES AND CLASSIFICATIONS.

     There is no such thing as a "correct" taxonomic name. Biodiversity names are always "opinions", and nothing more. How people choose to use them usually gives them "standing"; most names stand up well, even for centuries. No scientific name ever goes permanently out of use: an ignored name might yet be brought back into use if an expert publishes it in as a revised idea. When experts disagree, more than one scientific name can be in use at any time and users need to choose. With BioLists aiming for name stability, one is chosen more or less arbitrarily (and this can change for the next Year-version).  In scientific publications, each species name is accompanied by the name of the author whose opinion is being followed, eg "Lilium redeye (Smith)". Watch out. Given new evidence or ideas, experts are free to change their minds - so the year of publication is appended to the names of these authors. "Lilium redeye (Smith, 1999)" and "Lilium redeye (Smith, 2001)" could be two different species of Lily, but then one would be a wrong name - a synonym.

     BioList users need not bother with these issues; BioLists has them sorted before the names enter the database, and, by design, these issues are not critical for BioList users.

     Similarly, systems of Classification are complex works of the imagination promoted by fallible experts who work hard to make opinions that will last (and to out-compete rival experts). With BioLists, all Classification will be reassessed in making each new Y-v.

     For the future, Taxonomy will need to be more available and better understood so as to be of greater general use than it has been. Starting soon, we need to get serious about biodiversity issues and able to service ecology and conservation. But there will not be enough professional ecologists to do all the field data collection  that could be of use. The communications function of taxonomy is central to its utility. The BioLists' answer is to speed up all aspects of taxonomy and management of its data, especially raw data capture, in fact, to "do" most of the taxonomy so that ecologists need. James Lovelock's ideas on "accelerated evolution" could apply here - taxonomy keeping abreast with the new regime of information needs. [Lovelock. 2014. "A Rough Ride to the Future."]. First, the whole Taxonomic system needs to be effectively stabilized, but without disrupting research and existing taxonomy. To this end, BioLists has devised a way of standardizing taxonomic names and their classification for every-day use by non-experts. The system is purely for the convenience of non-experts. It does not want its use of names to be in competition with the professional Linnaean System. BioLists' names are "suggestions" for the names users want to put into lists and to mean what other users expect.

    BioLists needs to be used within defined limits: That's all.. It's critical to realise that there are no correct or incorrect taxonomic names; they are all only opinions. Similarly for Classification, users of taxonomy must know that there is no perfect system for ranking or sequencing names; all systems are always open to change. By conforming to a code, individual users can benefit from having a stable system in exchange for the freedom to have esoteric preferences.

     A major aim of BioLists is to help users get the checklists they want - every name they want. It is expected that most users of taxonomy. most of the time, will want to create and work with checklists that are compatible with those of most other users without question. BioLists can deliver this, within one limitation - the need for the classification to be in successive Year-versions (see below).
     On the other hand, the BioLists program makes it as easy as possible for users to key in any non-standard names. Alternative classifications and non-standard names will work within BioLists - just don't expect to work as easily with them, especially in merging or comparing files or relating to other peoples' BioLists files.

6.   YEAR-VERSIONS [Y-vs].

      BioLists inaugural Classification is called "Year-version 2000" (Y-v 2000).  It's a complete classified list of all ORDERS with a stable set of ORDER-Numbers. Every ORDER has its usable set of Families and, for starters, we've added all Genera for Flowering Plants and all species for a range of groups including Sharks, Frogs, Turtles, Sea Birds and Cetaceans (Whales, etc). Currently, all species can be checklisted from Y-v 2000 which is effectively "current" for most users because, as far as reasonably possible, the names used have been chosen to matches the texts and records that most people are using right now. Experts may well be years ahead for their specialist taxonomic groups.

     Adding all remaining Genus names to the BioLists' database is a top priority - and then as many species and Vernacular Names as users can send in. For now this Y-v 2000 will serve most people for most uses - and everybody's files will be compatible!. Already all species in all Families can be checklisted. Ideally search for Common Names: that delivers all formal taxonomy. Otherwise,  search for a Genus name, or its Family, and you can key in enough to make a complete record.

     The inaugural checklist, (Year-version 2000 (see below) which is still to have most Genera, species and Common Names added) will be followed by a more complete Y-v 2010 classification (currently this is only a part version for demonstrations).  New releases will be essentially complete (all Genus names and many species) and changes will not be made to them once they are released. Taxonomic changes will appear in the succeeding Y-v.

      Year-version 2010 is a partly updated version of the Y-v 2000 Classification. Already it can be used for new (post-DNA, APG-III) sequences for Flowering Plants and many ORDERS of Birds. Using this advanced classification is still a novelty in the academic world, so there is time to spare for BioLists to play catch-up.

      Next will be Y-v 2015, but it will not be relevant for a few years yet. It will be an edited update of Y-v 2010 (which will probably be called Y-v 2011 after it is finalised with inclusion of taxonomic changes that have passed expert scrutiny and been accepted into the scientific literature since about years 2012, or 2013. Thereafter, new Y-vs will be released as and when demand calls for them.

     Users should be aware that the Taxonomy in BioLists functions as a convenient, stable system only in the shadow of the professional Linnaean taxonomy. If you are publishing species lists or even just individual species names in a professional journal, then you must check the relevant publications for up-to-date names. Publishing names implies that you accept the reasons for considering them valid - in your opinion.

TABLE:    Biodiversity ORDER Numbers (BDV-#s) for 10 Plant species listed in two Year-versions.
                Cross-check between Y-vs to see their new classification relative to the other species.

     This Table lists the same ten species from each of the following two BioLists. (See also Note 8. below.)

File 1: NG-MEDIC-PLANTS-2000.csv  - - - download and edit these 159 Plant names.
File 2: NG-MEDIC-PLANTS-2010.csv  - - - download and edit these 159 Plant names.

     Each of these files contain all 159 species of plants named in:
Foster, S. and R.L. Johnson. 2006. "Desk Reference to Nature's Medicine".  US G. Soc., Washington. 416p.

     In the Table, note the differences in the BDV-#s (Biodiversity ORDER Numbers) between Year-versions 2000 and 2010 for the same ten species. The re-sequencing is because they have been re-classified relative to each other due to new information and understanding on plant relationships (mostly) resulting from recent DNA analyses. As one change, note that the Grasses (current 3298) have given way as "most advanced" to the Carrot Family (updated 3290)!

7.   BIOLISTS' FORMATS for Exporting/Downloading:
    
     The "WORKING format" is for data input to your BioLists (checklists). 
The following four file Formats can be viewed from the Working format during data input.

     Within the BioLists program, your checklists are in input sequence, but can be rearranged by clicking on column headers.   Clicking a column header reorgainses the whole sheet alphabetically (or numerically), or will invert it.

     The following four Formats can be downloaded to your spreadsheet program: your BioList remains in use in the BioLists program.     Your spreadsheet program will let you edit all aspects of the BioLists, but aim to retain compatibility with your other files by not changing BDV-#s.
   
     The "BASIC Format" lets you download and edit columns of general use.
     The "ECOLOGIC Format" clears space for species-level information.
     The "TAXONOMIC Format" gives best access to all the Latin Names.
     The "NOTES Format" makes room for you to best see and edit your Notes.
             Lengthy notes can have a (coded) summary in the leading 18 characters.
    
     Downloaded files are in Taxonomic sequence by ORDER-#, with nested Family, Genus and species sub-lists, in alphabetic sequence.
     The rearrangements show complete records (lines) in alphabetic (or numeric) sequence for the selected column.   Also, a column of Input Sequence numbers is present in downloaded biolists.

END of NOTES