BioLists Taxonomy
    The power of nature's names at your finger-tips.

First visit?  Sign up here



A  32-point  USERS' GUIDE

Your FIRST VISIT to BioLists?

1.  You've called up "www.BioLists.com" and found this page c/o "ABOUT" from the Home page or the tool-bar. So far, so good!
          Have you checked out other features on the Home page?  Before you "Log in" you can look into the database and other pages.
          Note the "Specimen BioLists".  One compares lists for Plant species for two Time-bands - current and up-and-coming Classifications.

2.  Also, before you "Log in" from the Menu Bar, you can see the names that are in the BioLists' database c/o "View DB":
          These are various lists of taxa (taxonomic names), initially in alphabetic sequence.
          To help search these lists, use the sub-menus, and change the sequence of their Records by clicking on the Headers - "BDV-#" and  "Names".
          Refresh (Cntrl-R) returns the original sequence.
          Numbers are BioList-defined ORDER Numbers ("BDV-#s = Biodiversity Numbers) in accepted taxonomic sequence for any Time-band.
          BDV-#s are for the Computer to sequence your Records; most users will have little need to refer to them, but at times they may be helpful.

3.  To register with us, click "Sign up".  Enter your Name and e-mail address; and a Password, and confirm this.
          Press "Next".   Then go see the Confirmation Email; click on the Link. - You're in.
          Return to BioLists' Home Page.

4.  The "Log in" box is now available. Enter your Email address and Password.
          Click "Log in". - Yes. Now you're really in.  Go to 5.
     NB: If needed, your email will be used to send you your password: your email address will never be used for any purpose outside BioLists.

                                             WELCOME!

Follow-up visits - Starting a new BioList:

5.  Click "Log in" on the Menu Bar.  Complete the Box as for point 4. above - and "Log in"
          You may "Log out" at any time: default 'Time-out' is after about two hours.

6.  To proceed, select "Your BioLists" from the Menu Bar.
          If you have existing BioLists, these are then listed. Go to 13 below.>
          Otherwise start your first BioList here:

7.  Start by clicking on "New BioList" and prepare to define its properties:
          Enter a "Name" for the BioList (this can be edited at any time).
          Select a "Time-band" (default is current = T-b 2000)
                 (Check out "Time-bands" from the Home Page  ("Notes - 6) and in "ABOUT/Innovations".))
          Note: The "Time-band" can be set only once for each BioList.

8.  Next, arrange to see Common Names in your choice of Languages:
          Utility and Tag names see (Home/Notes - 3.) are automatically put into species-level Records, but not if the species-level name is keyed in.
          These names cannot be keyed into a BioList or edited within the BioLists program; to do so download to your spreadsheet  (see 27.).
          All Utility Names are unique:  they complement other locality-specific and language-based Common Names.
          They are in the database for all Time-band (Year-version) 2000 species records.

9.  Vernacular Languages:  (See "Home/Notes - 4." and "ABOUT/Language List").
     Each time you start a "New BioList" (from the "Your BioLists" page), you may call up Common Names in one or two Languages of your choice.
          If none are wanted, just ignore the word "Blank", and move on to create your BioList.
          To select a Language, click on "Blank" (or its box), and a Menu of available Languages appears. Surf and select one.
          Repeat to select a second Language.
          The Language Menu can be seen in more detail on the "ABOUT / Language List" page.
               Note: Vernacular Languages can be set only ONCE for each BioList.
          In the database, each species can have zero to many Common Names in any of the named Languages.
          NB: Availability of Language-based names is sparse as BioLists gets started: Crowd sourcing will be encouraged.
               As yet, in addition to New Zealand English, we have Vernacular Names for only a few trial Groups: the main ones are:
                 -- all Aquarium Fishes (Freshwater and Marine), most Water Birds, and all Pigeons, Whales and Dolphins.
               The latter, the Cetaceans, have the widest range of Common Names; these are in several European languages.
         Some names in New Zealand Maori and Irish Gaelic are in the database: a few of these are shown in "Sample BioLists" from the Home page.
          If you work in a particular language with species in particular Families or Genera, then let us to make this easy for you and your team -
          Please send us long lists of Common Names - as a BioList in CSV (downloaded) format.  Please, do not send "Links".  First see "Contact us".

10. Note: one special "Common Name" is called "Species name"; it's the Latin binomen, ie the "Genus + species epithet", eg "Canis lupus".
          Selecting this, as either Language-1 (or Language-2), returns the Latin couplet for all species in your BioList.
          Your main use for this format will be in CSV files (in Excel, etc.), and for adding to e-mails and reports.

11. You are now asked to add a "Description of this BioList", ie to say what its content and/or purpose is.
          For field records, perhaps for ecology, think of this descripption as a label for one sample:
                 -- record the sample locality, date, and weather, etc., and name the collectors.
               Later, you can use "Edit" to add taxonomic naming authorities, literature references, or whatever ...
               Such samples can be ecologically significant, being a record of all species found together at one place and time. Useful?
        "Save" the above settings and the new BioLIsts is ready for adding names, etc.

And now for the interesting bio-bits:   Menus, and adding Names.

12. "Log in", select "Your BioLists" from the Menu Bar; see a menu of your BioLists;  and choose the one you want to work with.

13. The selected BioList appears in the "Find Names" page.
          Note the Box, top right, with the "File name", and the number of records in it ["Recs = n"], and , it's "Time-band".

14. When prompted, the BioLists program searches for names, both Taxonomic and Common (Vernacular; but not Utility or Tag names).
          These come up in a series of Menus, and the names you select from them go into your BioList.
          Note:  Menu names are displayed in conventional) taxonomic sequence at ORDER level and above: see "Higher Classification, 25".
            -- for example, Plants come before Animals; Birds come before Mammals; and Hedgehogs (9730) come before Rats and Mice (9990).
           Menu items are arranged alphabetically within ORDERS, Families and Genera.

15.  Here's how:  on the "Find" page, start to search for a particular name, Scientific or vernacular, (species, Genus, Family or ORDER):
         EITHER:  IF you don't know what sort of organism it is, then ignore the "Group Index:" and move down to the next line.
              At the "3-letter Prompt:" key in the leading 3 letters for the Name you want, eg "wol" for "Wolf":  then click "Find Names".
              This "3-letter Prompt" will return a Menu of all names in the database with those leading letters.
              Surf to find the target Name. You will not find "Wolf" but you will find "Grey Wolf" and "Red Wolf" - so you have to choose.
                     If the list is long,  you may use your browser's "FIND" option  (remembering these are in taxonomic sequence.)
              As the Database grows, BioLists will use a variety of strategies to keep the Menus manageable.
        OR:      IF you do know what sort of organism it is - its major Taxonomic Grouping - then click the Box for "Group Index".
              BioLists will return a Menu of 26 taxonomically-based Groups, A-Z. The default option is "All Groups". Select one.
                     This list shows the high level Classification used for all BioLists based on Time-band 2000.
              Having selected Group "Mammals", key in a "3-letter Prompt" for a particular species, Genus or Family.
                      For example: key in  "wol" for "Grey Wolf";  or "gre" for "Grey Wolf";  or "can" for Canis or Canidae.
                      These prompts will return a Menu to be searched to locate your target name.
                             Try "red" and "wol" and "can" to find "Red Wolf"

16.  Once you have found your target name, look up and down the menu near it - and not just at the leading names.
           BioLists searches the various levels within the Database, and for names within multiple names, as above for "Wolf".
                 It displays the names it finds in taxonomic sequence, (rather than alphabetically).
           As you accept names into your BioList record, their Higher Classification will show on screen;.
                 When you select a name above the species level, the program may display options for the next level of names;
                 for example, selecting a Genus name will show any species level names for it.
           Make sure you get the names you want;  ideally get them from the menus as a guarantee of compatibility with other BioLists.  
           Once satisfied with the Taxonomic part of the Record, move to the "Notes" box to add your important observations.
                  Add any species-related information and comments, then click "Add to BioList" to save the Record.
                  See 18, below, for when you may wish to look at all parts of the complete Record, and maybe Edit parts of it.                

17. The conventional taxonomic sequence used in BioLists' Lists and Menus is memorable, so it is useful.
           This sequence broadly defines accepted patterns of evolution as understood at the time of releasing the Time-band.
           Menus of names are sequenced in this way by allocated ORDER-level numbers.
     ORDER-Numbers are mainly for the computer to use. But, at times, you may find the numbers helpful.
           ORDER names and BDV-#s are not to be Edited or altered within BioLists!  Outside BioLists, take care at ORDER-level:
                 Don't merge CSV- files from different Time-bands; ORDER Names and Numbers can differ between Time-bands.
           These differences are important: the Numbers belong to different Classification Systems, aka Time-bands.
           Taxonomic changes reflect new research-level understanding of evolution; they bring names of closely related species together.
           Each taxonomic name, linked to its Classification, is a Key for use in searching for accumulated scientific knowledge.

Editing Records and BioLists:

18. Each "Record" in a BioList contains classified taxonomic names plus "Notes" that refer to it. Species are the usual subjects for Notes.
          All parts of any Record, including Notes, can be edited at any time. Click on "Edit" at the end of any Record in a BioList.
     In "Edit", all elements of the Record can be seen in full;  any item may be edited or added to.
          But note that ORDER Names and their BDV-Numbers cannot be Edited (see 17); nor should they be changed outside of BioLists.

19. BioLists makes it quick and easy to pick names from its database, or edit in the precise names they want to see in their checklists. BioList's database cannot, and does not, attempt to  accommodate all of the "available" names. That would be unworkable. About 1.5 million species have been described and named scientifically - but over 2 million names are in circulation. Many more "wrong" names (synonyms) are avaialbe (possibly ten time more for Plants), and, since any taxonomic name is simply an "opinion" of one author in a publication, any name may need to be revised. All published names remain in contention.

20.  What BioLists offers is a collection of middle-of-the-road, informal versions of Classification of the various Groups of organisms at different Time-bands (See: Home/Notes-6" and "ABOUT /Innovations") . No one such listing can ever be just what most users want. So, BioLists acknowledges this as a problem and faces it squarely. We assume that individual users will often want to use the taxonomy that is present in a particular favourite text, that a project leader may want to work with the taxonomy in a well-worn report or herbarium; students may want to use the names that appear in their course textbooks; research projects may choose to "fix" the taxonomy for the duration of a project, but knowing that all names will be updated before publication, and so on.  BioLists' flexibility encourages this by users selecting from the names that BioLists offers in the current Time-band - and then editing any items to conform to their wishes. So, BioLists is flexible and personal. But is this scientific! Yes and no. BioLists use of generally available taxonomies is pragmatic and user-friendly so as to achieve goals that otherwise would be impossible for most people if tangled up with nomenclatural problems - and all sorts of problems are inherent in taxonomy will never all go away - they will just change.  Taxonomies evolve as the various bits of the science progresses. BioLists' new thinking in this area means that you can hope to achieve much with the taxonomy at the expense of a little "roughness" - but, in BioLists, this roughness is under your control. BioLists' pragmatic use of taxonomy will make it easy for users to relate between conflicting professional systems of Classification. Skim the waves; nobody can control them.

21.  Your BioLists can be renamed, duplicated and deleted: this is done via "Your BioLists" from the Menu Bar in the "Select a BioList" page:
           Choose "options" for the relevant BioList, and then "Duplicate". This returns you to the "Select a BioList" page with the new copy added.
           You will want to rename one copy.  Already you have returned to the "Select a BioList" page, where this can be done - "Rename" the file.

Having created a BioList - now have fun with it:.

22.  As you add names to a BioList, your input sequence of names will often be more random than taxonomic.
           To make long name sequences searchable, ie predictable in relation to your understanding of conventional classifications,
                  click on the column header for the "BDV-#" [Biodiversity Number].
           The file gets rearranged in ORDER Number sequence (see 17 above).
      Within ORDERS, all nested sub-sets are arranged alphabetically, eg Family-, Genus- and species-levels.
           (Once BioList user groups are defined, taxonomic sub-groups may be made available as an option.)
      Clicking on the Header for any column (other than "BDV-#") in your BioList will arrange the Records alphabetically;
            Click again and the sequence up-ends.
                   Note: the Records stay complete across all columns.
      The column you are clicking on is now easily searchable - alphabetically.
      To return to a taxonomic listing, click on the "BDV-#" column; otherwise the program will revert to input sequence.

23.  Higher Classification: to check on this for any particular taxon, enter the initial 3-letters for any name into "Find Names":
          "Enter" brings up a "Names found" Menu; in it, search for the name you want.
                 clicking on accepts the name into the BioList, but see that it brings up its 9- to 12-part Classification: that is
          Gaia,  Kingdom & sub-Kingdom,  Phylum & sub-Phylum,  Super-Class, Class & sub-Class,  ORDER,  Family,  Genus & species.
          ("Add to BioList" accepts the ORDER BDV-# and ORDER name as well as the names below it into your BioList.
                This happens with the option to "Edit". Alternatives are to go "Back" or start a "New Search".)

24. Then there are the Common Names in each BioList record: 
          Species-specific Utility and Tag Names will appear automatically following species-level prompts; these cannot be edited within BioLists.
          Vernacular Names are also returned in your choice of Language(s).
     Note that with two Vernacular names selected, these translate the species names in both directions.
            
25.  Classification Systems. Similar to Taxonomic names, Biodiversity Classifications are "opinions"; they are all artificial, always provisional and never "right" (but can seem to be "wrong"); they are made simply for the convenience of Humans and computers. Their purpose is for communications, to summarise understanding of species' relationships so as to conveniently facilitate sharing of information about biodiversity. Some aspects of their contents have formal legal standimg based on a 260-year scientific tradition now enshrined in a variety of "International Codes of Biological Nomenclature".  The result is our evolving system of Biological Classifications and Nomenclature, that is, the over-arching science of Taxonomy and Systematics which, since Darwin and Wallace, attempt to relate described species within accepted theoretical ideas of Evolution. BioLists works within the rules to facilitate a useful, workable system for managing the accepted relationships between all known organisms.  Let's use Taxonomy pragmatically, at least until the present Biodiversity crisis is over - not just to tidy up documentation, but to be able to help Biodiversity recover by making good use of Ecology, and to help everyone understand and do good Conservation. This is probably the best way to help our species get through the present Sixth Mass Extinction Event - because we cannot do so without healthy, living ecosystems. Without our scientific understanding of taxonomy and Classification, Humans would be irrelevant as a global presence. But with wise use of taxonomy and classification, we may, by education, do useful ecology, such as defining and controlling the most noxious invasive species - not just ones, such as Stoats (Mustela erminea; 9710 - Mustelidae) in New Zealand that threated to radically alter ecosystems, but ones that need monitoring to determine their significance and for us to learn from them.

26.  As you enter species records into BioLists, you can append Notes for each species.
           These can record any aspect - location, time, conditions, etc, and, above all, your unique observations about this "sample".
           These "Notes" can be edited at any time.  On the other hand, you may archive BioLists as irreplaceable records.
           Unlike taxonomy up to now, your BioLists will stay fresh and usable, compatible within their Time-bands and easily updatable to the next T-b.

Exporting BioLists:

27.  From "Your BioLists" on the Menu Bar, you see a list of "options"; you can "Export as CSV" [Comma Separated Variables files].
                This gives your BioLists freedom, and wings - via the Internet!.
                Note: BioLists are downloaded (Exported) with their ORDERS in Taxonomic/Classified sequence.
           Family, Genus and species names are downloaded in alphabetic sequence
                In downloaded CSV files (but not (as yet) in BioLists), the ORDER Numbering is refined with decimalised sub-categories;
                This decimalisation follows the heirarchical structure of the actual file:
                for example, "3250.1.2.3" could be Allium sativum (Garlic) with "2" for a second Genus, and A. sativum the third listed species.

           Compare the Ecologic format in a download where Allium sativum might be listed as "3250-AMA-All".
                 This refers to "BDV-# 3250 which is the ORDER AMARYLLIDALES along with the Family Alliaceae.

           To "Export as CSV" click on the active "Create" key which names it - and the file has been created.
               Your original will still be available in your BioLists' account.

28.  Having created a CSV file from your BioList, it needs to be in a spreadsheet program for viewing, editing, and other spreadsheet functions.
           Use: "Right-click here and Save As". With this, your computer is likely to find a program to display it using "Open Link to New Window".
           It may well open in Excel.   Alternative "Save" options are available.
           (Spreadsheets other than Excel have not been tested: Feedback welcomed.)

29. In BioLists, the sequence of species-level records can be toggled between their input sequence and BioLists' taxonomic sequence. See: 17.
          To toggle Records by their code number, click on the column header "BDV-#" (Biodiversity Number):  click again to up-end the sequence. 
         "Refresh" (Ctrl-R) will return the input sequence.

30. Clicking on other column headers (except BDV-#), puts all species-level records in an alphabetic sequence, based on the column selected.
          Again, click the same header to up-end the sequence. This reversal between A-Z  and  Z-A can be useful for searching any column.

31. Similarly, a numeric list representing your input sequence of records is available in the right hand column of exported CSV files.
          As search features, points 29 above may be faster and more convenient than the generic "Ctrl F" function, but see...
          To alter the sequence of records in Excel, and to toggle these, and use Excel's sequencing function.

32. To Merge two BioLists, you need them to be in CSV format in a spreadsheet:
            -- first make sure they are of the same "Time-band" (upgrading may be needed) and that the columns are compatible;
                     then cut and paste one to join (concatenate with) the other;
            -- next re-sequence the pair by clicking on the BDV-# column and they become more-or-less seamlessly merged taxonomically.
          So as to be able to separate the files later, check that the numbers in the "Sequence" column would serve this purpose;
                otherwise put identifiers in the "Notes" column before merging.


All Best Wishes - for a Bio-diverse Future. Is anything else possible?

END of USER'S MANUAL