Prometheus User Manual
Contents
1. Collector SA Lugah ak Kudi lAmbriansyah lamer A rilara Beritiar num Dale of codec Me BE longitude A n 3 Latitude Figure 23 The Specimen input screen 2 6 Names In Prometheus it is important to distinguish between nomenclatural taxa and classification taxa Nomenclatural taxa Names are used to record the use of a particular name at a particular rank e g graveolens as the specific epithet of the Species Apium graveolens L Names in Prometheus do not represent any classification information and should not be used as such We believe that names are not a sufficient source of information to unambiguously identify classification groups as a single name might be used in different ways by different taxonomists The Name window is available from the Taxa menu Figure 24 Es GUI 0 2 0 rev 53 04 10 00 Taxa Dets Circumscriptions Descriptions Other Display Query Views Options Administrator 7 Rank People Publication Specimen Corrections Figure 24 The name menu 2 6 1 Input The name input window Figure 29 is one of the most complex input screens in Prometheus It not only allows the description of a name but also of its publication author placement and types At the top left of the window the rank of the name must be selected If the rank does not already exist in the database it can be added by clicking on the Rank button that disp2. Figure 53 Import text 5 2 1 Specimens The format of the file is the following Barcode tab Collectors tab Herbarium code tab Collection number tab Date of collection tab Location of collection Where tab represents the tabulation character 0x09 The authors must be separated by a coma Example EDOOSTOSO K Larsen T Santisuk E Warncke E 3407 14 08 1968 Empty fields must be represented and the preceding and succeeding tabs written 5 2 2 Classifications Classifications can be loaded from a text file 1f the structure of the file 1s as follows The first list of the file contains the authors of the classification E g Popper M F Watson Preston The second line contains the identifier of the classification publication E g Submitted to Botanical Journal of the Linnean Society Bot J Lint SOC The third line contains the date of publication of the publication E g 01 01 2000 Subsequent lines contain the name of a group then a tab character then the abbreviation of the author of the name then a tab character then the collectors of the specimen then a tab character then the description of the specimen E g Apium graveolens L J R I Wood 5761 E E00041057 5 3 HTML export Prometheus can export the contents of the database to an HTML file that can then be displayed in a browser Figure 54 r rq mmm ET 0 2 2 rev 55 31 10 00 File Taxa Dets Circumscriptions Descriptions Othe
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4. button will copy the selected classification and identify the new copy with the publication author information provided Once many classifications have been created they can be compared using the various visualisation tools provided see section 3 7 Copy a classificationn Classifications F Newman in M F Newman Thai Globba as a F Newman in M F Mewman Thai Globba as a PLU Adriansyah ugah ak Kudi Aambriansyah Publications __ Figure 43 The copy classification input screen 3 6 Canned queries During the process of creating classifications taxonomists are likely to have questions about various elements of their classifications ANILA Hired mar socia an tiere in The databrase LITT T Whai is the fs nd X7 Mel as Maret Erit probris ipid ie X T Whal nans bas Y pphished d e erst ihe specimens fori are cita ap N accierbng ts fl rot atop apmear ja Y eocoetbng ie AT Lint the specamers That arg lcd in X co e Add iuf net n Y acceding Lo AZ List the bgo that are iorfudnd in X acc So A1 er alse appear im Y accrerbng te A2 Whar spicaiirs aeg pur users on cssc atas KY Figure 44 The canned queries menu A certain number of these questions have been pre created in Prometheus because they are very common Figure 44 Although these questions are limited in that they are pre defined they allow a certain level of interaction with the database and provide answers for many useful questions such as what
5. This use of working names is important as it allows the description of circumscription taxa without having his opinion directed by the meaning he might attach to certain names The working name window is accessible from the Circumscription menu Figure 38 or from other windows offering this facility Es GUI 0 2 0 rev 53 04710700 File Taxa Dets Circumscriptions Descriptions Other Display Query Views Options Administrator Circumscription Generate Check Names Copy a classification Figure 38 The working name menu Working names are very similar to nomenclatural taxa names except that all the constraints attached to names do not apply to working names For example working names can have a type but do not need 1t as working names are not used for deriving names they are not validly published names In fact the only information that is compulsory is the rank information and the epithet g mem A F G Kerr Bulletin af miscellane H Wright Bulletin of miscellangss aralus Linnaeus Mantissa plan JAN Miquel Flora Mederlandsc AO Miquel Flora Mederlandsc Placement cerd Species cer Species cers Species Hap1 Species 2 Mame hap2 species Cancel nudi Species Validity Figure 39 The working name input screen 3 4 Naming a group hierarchy When classifications have been created and are at a stage the taxonomist wants to see what the calculated names are Prometheus can calcul
6. Kidi fiagellariz EU fragil amp SALI a gamebi Wer a geatka Gag a globulfera Ga a gramiifalla Inseciifera Fidi integra Ridl kerrii Cralb aL bal Globba laeta K Larzn Blobba leucantha Mi Globba macrucampa H Er maania L Gioobs nisbeliana Cr Globba nuda E Lara lobba obecura HKLa Globba patens Mig Globba pendula R en Figure 48 The TaxoVisu visualisation tool du MultHier To do 4 Backups for security reasons Prometheus manages a set of backups Every 24 hours Prometheus creates a new copy of the database that is stored in the Backup directory Prometheus keeps 10 backups at all times and replaces the oldest backup when a new one is created AA ar EA File Taxa Dets Circumscriptions Descriptions Other Display Query Views Options Administrator 7 Run backup Restore backup Delete backup Check consistency Switch objects Migrate to 0 1 0 rev 22 26 05 00 Reset names Export Dates Import Dates Figure 49 Backup menu It is possible to run the backup feature manually In the Administrator menu click the Run backup option Figure 49 The new backup will be stored with the others and backups that are no longer necessary are deleted In order to restore a backup for example after a wrong manipulation that resulted in inappropriate data that would take a lot of time to restore click on the Restore backup option A list appears that contain all the backups cur
7. clicking on the Author button At this stage Prometheus allows only one author for a given classification Circumscription taxa must also contain a publication information which represents the place of publication of the classification e g a botanical journal for published classifications or a dummy classification e g the date of creation of the classification for non published e g classifications created in the process of a revision classifications The need for dummy publication is simply for distinguishing classifications Indeed if one taxonomist creates two classifications because classifications are not necessarily a tree it can be multi rooted for example when the classification is created at Genus rank and below it would be impossible for the user and the computer to know which trees are part of the same classification e g Apium If the necessary classification does not exist it can be created by clicking on the Publication button Circumscription taxa must also contain a set of specimens for taxa at rank Species and below or a set of other circumscription taxa for ranks above Species Finally circumscription taxa may have an ascribed name and a working name The ascribed name represents the fact that either the classification has been published and therefore the names assigned to circumscription taxa are non changeable or the fact that the calculated name assigned to the taxon is not the name the taxonomist expected Th
8. constraints in Prometheus For example a name can only have one of a holotype a lectotype or a neotype exclusively but as many isotypes as necessary see ICBN for more information A name can also have only one placement as a name is a unique combination of its data In addition no name can have been published before 1753 because of a change in the way taxonomy works on that date names from the Series rank up must begin with a capital letter names at ranks between Genus and Species cannot start by Eu names of Families must end with aceae Subfamily names must end with oideae names at rank Tribe must end with eae Subtribe must end with inea names at rank Genus must not end in virus names at rank Genus must be in one word but can have hyphens d omg AP 2 6 2 Change Names can be modified In order to do so the taxonomist can click on the Change Name button and select in the list the name to be edited When the name is displayed in the window it can be modified and then saved Save button If the name has been used in a classification it cannot be changed as changing it would mean changing the meaning of the classification This is especially true when the classification has been created by a taxonomist other than the current user When names are changed they might affect the way classifications are named For example changing the type specimen of a name could mean that all classifications
9. naming of their higher taxa before their name can be calculated For example graveolens Species epithet must be placed in a higher rank taxon Genus in order to be resolved to a full Species name e g Apium graveolens Therefore when the calculation process starts the user is presented with the circumscription taxon that will serve as the start of the evaluation and all its lower taxa will be named re named The automatic calculation of names only considers holotypes lectotypes and neotypes According to the ICBN only these types are valid types for deriving names This could be a problem for older data created when typification rules were different The Prometheus system forces taxonomists to lectotypify so that the definition of names is valid regarding the ICBN rules If the database does not contain enough information to name all the groups that are to be named e g the circumscription taxa do not contain type specimens an error is generated and the user is warned of the problem He can then go back to the name description section section 2 6 and create the appropriate names or go back to the circumscription description and include type specimens Section 3 1 In some cases the database contains enough information to calculate the names but a new combination of a multinomial name e g Species name is necessary for example after the taxonomist has placed a Species group into a Genus group that results in moving a Species name to a
10. obtained Unlike when the user clicks with the right button on an element this synonymy is specimen based When the taxonomist clicks on the Info button after having selected the elements he wants to compare Prometheus shows their relationships in the display list at the bottom of the screen It tells how many specimens they have in common whatever the level of specimens is relatively to the selected elements the percentage it represents relatively to the total number of unique specimens in the selected groups 100 for complete synonyms and whether they are homotypical or heterotypical This feature is used mostly for 2 elements e g Apium graveolens L according to Tutin and Apium graveolens L acording to Popper et al If only one element is selected Prometheus searches for all the synonyms in the database This is useful to discover unknown synonyms especially partial synonyms AA 1 Im ut utet pones PL atn NES ug Ma aa VS ag BL eU ur uo Mis ee es a ioa Late Li ura Lite 7 ete ee ee ee ee ee ae ek aen URP gre Y ve TRI eee Uy LES Beige Skt habe sks abe GE AA sah gei pon gei pe ei Pa o s es es Le ee a thilus Hemel ry rhiluz ziarmurrtz H arepalla Horan erstanihera TLestib lobba albiflora Feel lobbs annamensis Giobba aphanarnma apreta Mig lobba barthel Gage looba bicolor Gagna Globba bubfera Ro Globba bulbosas Day Eis calopiilla Ri E cambadiensl a candids Gag a camua Bake clamei Baker colgo En Tazciats
11. operation is very dangerous Ranks are used in many places Do you want to continue Hame Aa mnm mamas Prenoas Hank u Next Hari Genus Genus section section SPECIES Species vafe ariete Figure 7 The rank input screen 2 3 People In Prometheus People represent any human being that is to be represented in the database This includes taxonomists and specimen collectors People information is essential to the working of Prometheus as they are necessary to the display of taxon names e g Apium graveolens L and to the description of specimens e g K Larsen AAU 10095 1963 This editing window can either be called from the general menu Figure 8 or from various other input screens ES GUI 0 2 0 rev 53 04 10 00 File Taxa Dets Circumscriptions Descriptions Other Display Query Views Options Administrator Publication Specimen Corrections Name Figure 8 The people menu 2 3 1 Input The People input screen Figure 14 allows the description of five types of information relating to People First the surname of the person can be described This is the only compulsory information to be supplied Then the given names first name and or initials can be described The abbreviation for an author can be selected in the list below If the abbreviation does not already exist it can be created by clicking on the Abbrev button A new screen will appear that will allow the description of a ne
12. that use that name must be renamed If this occurs Prometheus displays a message Figure 26 that tells which circumscriptions see section 3 1 must be checked or renamed It is possible to do so using the Generate Check names feature see section 3 4 m Check namez x The following circumscription taxa need to have their name recalculated Basicalcaratae K Schum according to Karl Moritz Schumann in Karl Moritz Schumann Das Pilanzenreich MW 46 1904 Figure 26 Check circumscription message 2 6 3 Delete Names can be deleted by first selecting them by clicking on the Change Name button and choosing the appropriate name in the list of names then by clicking on the Delete button The deletion of names 1s a very sensitive matter Indeed deleting a name might lead to the impossibility to name classifications When the taxonomist requests the deletion of a name a warning message is displayed in order to remind him of the importance of the operation Figure 27 In addition 1f the name has been used in a classification an additional warning explaining the dangers and the consequences of the operation is displayed Figure 28 If the taxonomist wants to proceed to the deletion the name is deleted and all information about it is lost mn Warming Deleting an object might imply deleting many objects Are you sure you want to continue Tes Ho Figure 27 Name deletion warning 1 igi The Guru s advic
13. the deletion of publications d 7 o IAM should be performed very carefully When the deletion order is sent the database checks whether it would be safe to delete the publication If not it displays a message such as the one shown in Figure 18 En The Guru s advice this operation is usually safe However this instance of publication seems to be used by other objects in the database Therefore loss of data may occur if you continue Do you want to continue Figure 18 Warning message for publication deletion Note that when publications are deleted from the database the information they are used by e g name descriptions is not deleted 1f possible Edit Publication Hew Publication Change Publication Reference Abbrev Asiat Res APH Hat Mag APH Clear Bull Misc Infarm APH Date Page lt a a Figure 19 The publication input screen 2 5 Specimens Specimens in Prometheus are at the centre of the taxonomic process They are both used in the naming part of the process creation and derivation of names and in the classification side of the process They can be edited in a window available in the Taxa menu Figure 20 GUI 0 2 0 rev 53 04710700 File Taxa Dets Circumscriptions Descriptions Other Display Query Views Options Administrator Rank People Publication Corrections Hame Figure 20 The specimen menu 2 955 Input The description of specimens
14. the taxonomist can save the information by clicking on the Save button If the information 1s not saved in this fashion it will be lost If the new rank that has been described already exists in the database a message saying so will be displayed and the data supplied will not be saved see Figure 5 If the taxonomist does not want to save the information clicking on the Cancel button will lose the input information zd m Creation error This rank already exists Figure 5 Duplicated data message Note that the links between ranks are automatically updated so there is no need to update the next rank information of a rank after another rank placed directly below it has been added to the database 2 2 2 Change When data has been input in the database it is possible to change it For example it may be necessary to change a rank description because a new rank is necessary and needs to be inserted in the rank hierarchy To do so the taxonomist can click on the change rank button A list of all existing ranks will appear and the rank to be changed can be selected either by double clicking or by selecting it and clicking on the Set button Once the rank to be changed has been selected it will appear in the main ranks window where it can be described Once the changes have been made the taxonomist needs to save the changed by clicking on the Save button If the Cancel button is clicked the inf
15. 1875 C H Wright Bulletin af miscella SAL J F Maxwell 1969 Carolus Linnaeus Mantissa pl SAL J F Maxwell 13858 FAY Miquel Flora Nederlands SALI P Bunma 1967 Hapi Species RAW Miquel Flora Nederlands SAL S N Chong 1970 hapz species FAW Ms Flora Mederland MAU 1 D Vincent 1378 nudi Species CX ni Hud E Larsen Species T y Eu ES Figure 37 The circumscription input screen momo Xm 3 2 Creating existing classifications During the process of a revision it is often useful to be able to compare the classification being newly created with existing published classifications The groups from existing classifications are entered in the same way as new groups in the circumscription screen see section 3 1 and Figure 37 These classifications as they have already been published have fixed names attached to the circumscription groups Therefore when such a group is entered an ascribed name must be chosen This name should be the name that has been assigned to the group by the author of the classification even if this is a misuse of the name When the group is saved a name calculated from the available data is also assigned to it automatically Complete existing classifications can be created by building them block circumscription by block 3 3 Working names As explained in the previous section working names are used by taxonomists when they create classifications using groups that have not been named yet
16. Change All the groups created circumscriptions can be changed if necessary To do so the taxonomist can click on the Change Circumscription button and select the circumscription to be changed When all the changes have been made clicking on the Save button saves the changes The changes may affect existing classifications For example they may imply that the names that have been attributed to a particular circumscription are no longer valid If so Prometheus displays a message that lists all circumscriptions that need to be checked or renamed Figure 36 The check can be made in the Generate Check window section 3 4 If the checks are not made before Prometheus is shut down the same message will appear the next time Prometheus is started The berri ze cemsaz ri ian taza zzz de hee ther zai caca Mom a o gs Hoi mc cdd iir do RIT Porn p jc Bats gest a cd MAL Se DSi ges oes rb aco onn fy bo cT issus cube aea Er doraa in Bo 9 ow Sis Sect in ss Eae Scena fie Plane Pa diente h Tate Lin 85 ar Mer zr in Earl Werkes Schein Das Prbrverrmiza Be a IL paid Pd Sl es ILLI A mince fg a IET p Jr MIL IILIU ape vera Hora acord e Hae Br d e rn ec ae Metz Schnee Des Pere cid hi 28 TR hie racer en ecards iz Ear Made churro iz Fac leds Sc hora Doo Parca pic b Ps 58 EAH Tea C Even Hades co He Fas Bec Sa Taie in Foe Pr a pid esie Des Decus gen Fs Fur 3 1 EUG Boer gs alae Hi iic ceniby i Pert bha Ex basses da Srt Eon T 3c ae
17. Prometheus User Manual Version 0 0 2 25 01 01 11 11 C dric Raguenaud Dr Mark Newman cedric dcs napier ac uk M Newman rbge org uk School of Computing Royal Botanic Garden Napier University 20A Inverleith Row 219 Colinton Road Edinburgh EH3 5LR EH I4 ILT Scotland UK Scotland UK Contents l 2 6 Modi LOT aca seine a tutt een te cere ere 4 Enter CX SITS qat deseen von dal cele bein e epe mieu 4 2 1 Generalmtormation onmall WinGOws iure tone ix On be sese ert ee EE SE EUREN UIS acess 4 2 AR AMM ead ss eseteotast auta t Dux EE M UM INT CE M ML E Metu 5 22 A A 5 Za Lodo A 6 2 2 5 IBI RUE 6 DiS O 7 223 1 ojos e M 8 229525 A A RO NA 9 2 3 9 Delete 10 22 A usaron tee ceria iude Teen HAC em ne Rare a te Nora terre emery EHE p UE 11 2 4 1 boire REPE 11 2 4 2 Bini M M 12 2 4 3 A Dueh a eee he eats cel ad alata Ua c Eos toutou 12 Le SPECIES 13 2 51 DUNC ec 14 22 A ne ER Lo i MEUSE A OE ELM ID E ER 15 2I Dt diana AA N M E 15 AO NAMES ET IU UU TUE 16 2 6 1 o DA A epe LU Ee 16 2 6 2 A m lauiie tev eeieie ds 18 2 6 3 Dele uu o tii bist m cC etos iiu a eh Tee cens 18 2 HEOTFECMON Si wen ao Sete d v nena vites rtu oup fa aoc T E NNER 20 2 1 4 jaro EE EE AEE E E E dd da de 20 2 52 Cabernet ditum uA Stt nud us dtu LEM odit eu
18. abase is displayed The sort order for these is alphabetical order for names nomenclatural taxa alphabetical order for working names then alphabetical order for specimens i e the list has three parts one for each kind of objects In the middle the main display which is explained later on At the bottom in the middle a list of all defined classification trees is displayed Each described in a small box and with an individual colour Note that these are trees not really classifications i e if a classification contains many trees many boxes with the same name will be displayed 3 1 1 Above this list there is a blank list with 4 buttons The Hide button removes elements selected in the main display Show re displays them and Info gathers information about the selected elements When ranks on the left are selected by clicking in the box next to a rank name all elements in the database at that rank appear in the middle display If many ranks are selected the display shows a nested display of these elements at the required ranks For example if the taxonomist chooses Genus and Species he will see a few boxes appear that represent Genera their colour corresponds to the colour of their classification in the list at the bottom of the screen and in each of them smaller boxes that represent Species Only the Species that appear in the genera that are displayed are shown i e if a Species CT has been created and has not been cl
19. an author abbreviation and not replacing it by a new one will impair the normal display of taxon names as author abbreviations are to be used Edit People Abbreviation Hew Abbreviation Change Abbreviati Abbreviation BPH Origin Brummit amp Powell 1992 Clear pe Cm e ou Figure 10 New author abbreviation screen The addition of a new source for an author abbreviation is made in the window shown in Figure 11 The only information that is required is a textual description of the name of the source of the abbreviation e g BPH TL2 Once the information as been input it can be saved using the Save button Once it has been saved it will appear in the list of the abbreviation window A source of abbreviation can be changed by selecting it Change Database button and then saving it Save button It can also be deleted by selecting it and then deleting it Delete button The deletion of a source of abbreviation does not have consequences on the general functioning of the system Figure 11 Adding a source of abbreviation At the bottom of the edition screen a Find button is provided The purpose of this button is the display of existing persons according to the details provided For example in order to check whether a person of name Linnaeus has already been defined in the database the taxonomist can input Watson in the surname field and click the Find but
20. arning messages can be safely ignored However if only one window is open and the message appears it means that an error has occurred in the database and some data has not been saved The safe approach is to close Prometheus and run it again and report the message and the circumstances to the administrator A A transaction was already opened and it was unexpected Vill use it but the main transaction might never be committed Figure 2 Opening message No lists in Prometheus are resizable However when the mouse is passed over contents of the list a dynamic purple box called a tool tip appears and displays the contents of the list line beneath the mouse Figure 3 Figure 3 Tool tip example 2 2 Hanks When Prometheus is installed the database is empty The first stage is therefore the description of ranks The window can be called from the Taxa menu Figure 4 T 0 2 0 rev 53 04 10 00 File Taxa Dets Circumscriptions Descriptions Other Display Query Views Options Administrator People Publication Specimen Corrections Hame Figure 4 The rank menu 2 2 1 Input In Prometheus ranks are chained from the top to the bottom from Regnum to Subforma As in taxonomy not all ranks are mandatory in Prometheus As the taxonomist describes new classifications new ranks can be added For example it is possible to start using Prometheus with simply a Genus and a Species rank if these are the ranks of interest of th
21. assified in a Genus CT and the taxonomist chooses to display the Genus and Species ranks the Species taxon will not be shown The taxonomist can select and unselect various ranks as required When the mouse is moved over the main display the name of the object under the mouse appears in a tooltip boxe and in the list display at the bottom of the screen If the user clicks with the left button on one element on the screen it becomes dark blue As many elements as necessary can be selected by keeping the Control key pressed and selecting many elements sequentially It is useful for example if the user is not interested in these elements and wants to make them disappear In that case once the undesirable elements have been selected a click on the Hide button and they disappear If the user wants them back a click on the Show button makes them reappear By clicking with the right button on an element 1t becomes red it 1s highlighted in the display on the right hand side of the window and all occurrences of its calculated name occurrences in various classifications will become red on the screen All occurrences of its ascribed name if it is defined will appear in black in other classifications It is also possible to make elements become red by selecting them in the list on the right hand side This shows nomenclatural synonyms in various classifications When one or more elements on the screen are selected synonymy information can be
22. ate these names and assign them to circumscription taxa GUI 0 2 0 rev 53 04 10 00 File Taxa Dets Circums riptions Descriptions Other Display Query Views Options Administrator Working Hame Circumscription Copy a classification Figure 40 The generate check names menu The selection of the groups to be calculated is done in the list that appears in the generate check names window Figure 41 available in the Circumscription menu Figure 40 This list contains all circumscription taxa defined in the database whether they have already been calculated or not This is due to the fact that it is sometimes necessary to recalculate a name e g after a nomenclatural taxon name has been modified or after a circumscription taxon has been placed in a new higher rank taxon e g a Species circumscription taxon placed in a new Genus circumscription taxon Once the circumscription to be named has been selected in the list the taxonomist can click on the OK button and the evaluation will start The checkbox called Display all names switches between 2 displays The display of only the circumscriptions that need to be checked or renamed default checkbox unchecked A p 78m The display of all circumscriptions The calculation of names is a top down process i e it must start from the highest taxon and proceeds down the classification hierarchies This is largely due to the existence of multinomial names that require the
23. ayed in the list at the top right of the window 2 8 2 Change In order to change a determination the taxonomist must first select the det to be changed by clicking on the Change Dets button and select the determination to be changed in the list of all determinations Then when the information relating to the determination is displayed it can be modified Finally changed can be saved by clicking on the Save button or discarded by clicking on the Cancel button 2 8 3 Delete Determinations are deleted by first selecting them by clicking on the Change Dets button and then pressing the Delete button The taxonomist is the presented with a confirmation dialog window Figure 33 explaining that the deletion is a save operation 5 The Guru s advice it seems pretty secure to continue with the operation Do you want to continue Yes Ho Figure 33 Determination confirmation message AA IAM Change Dets eratanthera T Lestib sec a Figure 34 The determinations input screen 3 A Revision In this section we present how a taxonomist using Prometheus can represent classifications and proceed to the revision of a group We assume that the database already contains information specimens names and classifications relative to previous classifications of the group This information can be imported from an existing database 3 1 Creating a group When a taxonomist desires to creat
24. d When all information has been input it can be saved by clicking on the Save button If the operation must be cancelled click on the Cancel button The display of names is described in the ICBN For example Species names are binomial names that must consist of a Genus name followed by a Species name plus author information Subspecies names must consist of a Genus name followed by a Species name and then the Subspecies name Because these rules might change over time or are not clearly defined in the ICBN Prometheus uses an external file to describe such rules It can be found in the root directory of Prometheus and is called namingrules txt Figure 25 shows an extract of this file The first part of each line before the colon represents a rank name and specifies that the rest of the line describes how names at this rank should be displayed Then after the colon a succession of words and rank names is given A rank name between square brackets represents the specific epithet of the name at this rank and a word without brackets a word that must be displayed unchanged For example Variety names must be displayed as a Genus name followed by a Species name the keyword var and then the Variety name The name for each rank is found by going up the placement hierarchy starting at the name to be named Genus Genus Species Genus Species Variety Genus Species var Variety Figure 25 Naming rules Names are subject to
25. d Cheb Pr enr bs Fa 6b d SOR ds ma ambu seri da Kari Erir Er horas in Earl Berri e Er borre Dax Pale b Ig SN IS quta A 0 ga AO ROS pem 1 RH MA ri Ds PIE ei deeem BE dE ADA Ip BRL ngo rLpLL rpuS JL ipe E au nip o It d cima L serzitywi sr Harris Hae an cr rm xau Spr Seen in Hari ca Schoen Dar Hirea S AE 894 xrrdegis Baci Rar churn m kad fiir chan Dax Pree 722582 kokrra Goo seceding 2 ardor Se hores in Pal a St hema es PL am canet F 4p AO Figure 36 Circumscriptions to be checked 3 1 3 Delete Circumscriptions can be deleted To do so the taxonomist can select the circumscription to be deleted by clicking on the Change Circumscription button and selecting the appropriate circumscription Then clicking on the Delete button deletes the circumscription If the circumscription is involved in a classification Prometheus warns the user of the fact that it may be a dangerous operation and that it may imply renaming many circumscriptions If the taxonomist goes ahead with de deletion Prometheus deletes the circumscription Prometheus also displays the circumscriptions that will be affected by the operation and requires the user to check that the names that are attributed to these groups are correct Figure 36 Achilus Hemsl Genus Achilus siamensis nito Careyella Horan section Ceratanthera T Lestib section Globba albiflora Ridl Species Globba SEU SG MIA AFG Kerr Bulletin of miscellar SAL B Rogers
26. e this object is used in a classification strongly advise not to delete it Are you sure you want to continue Tes Ho Figure 28 Name deletion warning 2 Publication Clear FG Kerr Bulletin of miscellane H Wright Bulletin of miscellane 2 Carolus Linnaeus Mantissa plan AWW Miquel Flora Nederlandse AM Miquel Flora Mederlandsc Adriansyah ugah ak Kudi arevella Horan section eratanthera T Lestib section Name lobba albiflora Ridl Species Validity Figure 29 The name input screen 2 7 Corrections Corrections are used in taxonomy to specify that an author has made a mistake in a publication e g misspelling But because once some data has been published it is illegal to change it no correction can be made Therefore Prometheus offers a mechanism that allows the description of correction without changing the actual data E GUI 0 2 0 rey 53 04 10 00 Tas Dets Circumscriptions Descriptions Other Display Query Views Options Administrator Rank People Publication Specimen Figure 30 The correction menu 2 4 1 Input Any object on Prometheus can be corrected Therefore in the correction window Figure 31 all objects defined in Prometheus are displayed in the list at the top left corner of the window The object to be corrected must be selected in this list Then the taxonomist chooses the person responsible for the ANILA correction in the list on the ri
27. e changes discarded by clicking on the Cancel button 2 9 9 Delete The deletion of specimens is a dangerous matter Indeed because specimens are used in the creation of taxonomic names and in the creation of classifications the deletion of a specimen might invalidate a name e g if the specimen is the type specimen of a species or render Prometheus unable to name a classification taxon because it no longer contain a type specimen However the deletion of specimens is possible When a taxonomist wants to delete a specimen he can click on the Change Specimen button and select the specimen to be deleted When the appropriate specimen is displayed it can be deleted by clicking on the Delete button When the deletion order is sent a confirmation message is displayed in order to make sure that the taxonomist is aware of the risks of deleting a specimen In addition if the specimen has been used in a classification or as a type the message recommends to re calculate the names assigned to classification taxa Figure 22 If the deletion is confirmed the specimen is deleted m Warning igi The Guru s advice this is not usually a dangerous operation However this specimen is used by other objects therefore loss of data may occur if you continue You should generate check names again after the operation Do you want to continue Yes Ho Figure 22 Specimen deletion warning A PI
28. e classification descriptions the basic unit that can be described is the circumscription taxon A circumscription is a group of specimens or other circumscription taxa according to criteria that are important to the working taxonomist Circumscription taxa are to be distinguished from nomenclatural taxa as circumscription taxa are not immediately named and their name can be derived automatically by Prometheus The circumscription window is available from the Circumscription menu Figure 35 RA GUI 0 2 0 rev 53 04 10 00 File Taxa Dets Circumscriptions Descriptions Other Display Query Views Options Administrator Working Name Generate Check Names Copy a classification Figure 35 The circumscription menu RA ILA 3 1 1 Input The circumscription input window Figure 37 allows the description of a single circumscription taxon By describing many nested circumscription taxa the taxonomist can create classification hierarchies Each circumscription taxon must be placed at a particular rank This is specified in the rank list at the top left corner of the window If the rank required is not already defined it can be created by clicking on the Rank button that displays the rank edition screen see section 2 2 Circumscription taxa also contain a reference to an author who is the person having published the classification or created for unpublished classifications If the necessary person does not exist it can be created by
29. e user The input screen for ranks is divided into four main parts see Figure 7 At the top an input text box allows the description of the name of the rank e g Genus Then below that box the taxonomist can describe whether the rank is multinomial or not using the multinomial checkbox Multinomial names are names that contain more than one word as the result of the application of the ICBN Greuter et al 2000 to the data For example Species names are binomial therefore multinomial and Subspecies names are trinomial therefore multinomial The rules to derive names are not described at this stage and are stored elsewhere in Prometheus Below this checkbox two lists are displayed They all contain the names of all the other ranks already described in the database In order to add a new rank the taxonomist must select the rank that is going to be directly above it in the hierarchy in the list on the left and the rank that is going to be the next rank in the list on the right For example a Genus rank can be described as being placed below a Family rank and above a Species rank Therefore the taxonomist can describe Genus in the text input box the select Family in the left hand side box and select Species in the right hand side box The Clear button above each list unselects any selected element in the list beneath it The only information that is compulsory is the name of the rank Once all the information has been input
30. e working name is the name that is used to identify circumscription taxa before they are named Indeed before a name is calculated by Prometheus circumscription taxa should not be named in order to avoid the preconceptions attached to names that would impair the creation of a purely specimen based classification process If either of these names do not exist they can be created by clicking on the Ascribed or Working buttons For example if a taxonomist was to create a classification containing a group representing Apium but not necessarily called Apium at this stage and a group representing Apium graveolens the following groups would be created A Firstly a circumscription taxon that contains the specimens grouped in what will become Apium graveolens in particular the type specimen so that the name of the group can be automatically derived later This group would be a Species rank group only groups at rank Species and below can contain specimens Secondly a group at rank Genus containing the previously created group and possibly some additional groups e g Apium repens At the stage when these groups are created they may not be named as the naming of groups might depend on the other groups present in the classification e g Species groups depend on the Genus groups they are placed in The conjunction of these two nested groups the first one is placed in the second one forms a small two level classification Sse
31. ecies on the specimen sheet Although these determinations do not carry classification information and should not be used in a classification they provide an insight into what a particular taxonomist was thinking when creating his classification Prometheus therefore offers ways to record these determinations Figure 32 43 7m T 0 2 0 rey 53 04 10 00 File Taxa a Descriptions Other Display Query Views Options Administrator 7 Figure 32 The dets menu 2 8 1 Input The dets input window Figure 34 is divided into two parts the top and the bottom part The bottom part is used to enter data In order to input a determination the specimen that was determined to a name must be first selected in the list of all specimens in the window at the top left of the window Then the author that is responsible for the determination is selected in list at the bottom left of the window Then a date must be input if available in the text box at the centre of the window And finally the name to which the specimen has been determined must be chosen in the list of all names in the list at the bottom right of the window When all the available data has been described it is saved by clicking on the Save button Existing dets can be seen by first selecting the specimen that is studied in the list at the top left of the window then clicking on the See dets button at the right of the list All existing dets for that specific specimen will be displ
32. ens in the process of a revision will originate from a herbarium They are also likely to have a collection number unique in their herbarium Although these fields are important they are optional In addition to this information specimens may have a date of collection which can be of the form day month year month year or year a latitude and longitude data Finally specimens can have a text attached to them that can be anything the taxonomist desires the Latin description of the specimen additional collection information such as altitude or general comments The input of information is completed by clicking on the Save button that will save all the data and reset all input fields Note that specimens are displayed in an unconventional manner in lists The display consists of first the herbarium then the collection number then the list of collectors and finally the year of collection e g P 410 Geoffray 1904 The reason for this display order is the search in large lists of specimens We have assumed that the most common pieces of information available about specimens are the herbarium of origin and the collection number By displaying this information first the search in lists is made more efficient Specimens should be uniquely identified entities in taxonomy In an ideal situation this uniqueness is provided by a barcode as is the case at RBGE However not all herbariums do not provide barcode systems for specimens therefore spec
33. ght side of the window generally the taxonomist himself and writes the text of the correction in the text box at the bottom left corner of the window Once all the data has been input it can be saved by clicking on the Save button If the information is to be discarded the Cancel button is used 2 1 2 Change Corrections can be changed by selected the correction to be modified in clicking on the Change Correction button and choosing the correction in the list of all corrections The correction is then displayed in the window and can be modified When the modifications are done they can be saved by clicking on the Save button 2 7 3 Delete Corrections are deleted by first selecting the appropriate correction in clicking on the Change Correction button and second clicking on the Delete button The deletion of corrections is safe for the system and does not have consequences for the rest of the database Hew Correction Flement to be corrected Author Adriansyah ugah ak Kudi Ambriansyah a y m 4 mS BEES SE Wh ftit ftu fu tutu Correction SS COREA A tete Rat eta a a ee a a e a E e er E Latest atat ata ate ta sew o om o tm Figure 31 The correction input screen 2 8 Dets Dets represent the determinations that can be found on herbarium sheets When taxonomists work on a classification they sometimes write what they think a specimen is e g the name of its Sp
34. gnored If the specimen to become a type does not exist it can be added by clicking on the Specimen button that will open the specimen edition window see section 2 5 If a name that is to become a type e g a type Species does not exist it can be added by clicking on the Name button that will open another name edition window Multinomial names e g Species need a placement in order to be valid For example the Species name graveolens can be placed in the Genus Apium in order to form the full Species name Apium graveolens The placement can be selected in the list at the bottom left of the window For example for Apium graveolens the name graveolens is placed in Apium Note that placement information is a not classification information It only records the use of the combination of Species name and Genus name Finally names have validity information Validity represents the fact that the name has been validly published Because the rules of publication of the name cannot be checked by a computer the abstract validity flag represents the statement by the taxonomist that the name has been validly published Only validly published names are used for the derivation of names The compulsory information is rank epithet publication and author Other information e g type is optional but may have an influence on the functioning of the system e g no type information will result in the discarding of the name when names of taxa are derive
35. he WEB PAGE field contains the main address of the project The SERVER field contains the full address of the HTTP server The SERVER PAGES contains the path from the Prometheus Server HTTP to the pages that the server can display The HEADER field contains the header that will be inserted at the top of all pages and the FOOTER field contains the footer of all pages Finally the SHUTDOWN PASSWORD contains the password to shutdown or restart the server remotely WEB PAGE http www dcs napier ac uk prometheus SERVER httos 1923 52 15441390959 SERVER PAGES pages HEADER center table BORDER 0 COLS 2 WIDTH 100 gt lt tr gt lt td gt lt img SRC smprometheus jpg height 160 width 102 gt lt td gt lt td gt lt div align right gt lt font size 3 gt Prometheus Web Server lt font gt lt div gt lt td gt lt tr gt lt table gt lt center gt FOOTER lt center gt lt table BORDER 0 COLS 2 WIDTH 100 gt lt tr gt lt td gt lt a href gt Home lt a gt lt br gt lt a href info html gt Info lt a gt lt br gt lt a href action version gt Version lt a gt lt td gt lt td gt lt div align right gt lt a href SWEB_PAGES gt Prometheus Project Page lt a gt lt div gt lt td gt lt tr gt lt table gt lt center gt SHUTDOWN_PASSWORD napier Figure 51 HTTP configuration file A few modules have been written and are provided as built in modules in this version or Prometheus These modules allow the disp
36. he abbreviation optional If the source of the abbreviation is not already described in the database a new source can be added by clicking on the Origin button see below When the available information has been described it can be saved by clicking on the Save button An existing publication abbreviation can be modified by clicking on the Change Abbreviation button and selecting the abbreviation to be changed Once the changes have been made they can be saved by clicking on the Save button An abbreviation can be deleted by selecting it first using the Change Abbreviation button and then clicking the Delete button Note that deleting a publication abbreviation and not replacing it by a new one will not impair the normal display of taxon names as publication abbreviations are only used for reports 4 34 P 7mm Edit Publication Abbreviation Hew Abbreviation Change Abbreviation Abbreviation Origin BFH Brummit amp Powell 18387 TL Clear Save Delete Cancel Figure 16 Publication abbreviation screen The addition of a new source for a publication abbreviation is made in the window shown in Figure 17 The only information that is required is a textual description of the name of the source of the abbreviation e g BPH TL2 Once the information as been input it can be saved using the Save button Once it has been saved it will appear in the list of the abbreviation
37. heck cicturnsettpHOonD Messi ia Mops Pei 18 Dioute 27 Name de lemon warnine ii eom E eint a ots eee uui DAD 18 PE150re 25 Name deletion ed NE NETS 19 A a eo AAA ette iue eed feces 20 Eisure 0 Ehe COME CMON Te DU ta a ei aho ien ocd oa EAA 20 Fisure SI The COME chrom THpUC SCTOOB ere ood Hv e RU o eo munia ia dove dua qe NUS 2 LEr5ure o2 mne gets qHellll teo do E DIS LL S EN LE E E Eten 22 Figure 33 Determination confirmation message esses eee teeth enne netten nnne tn nennen nennen 22 Figure 24 The d termianatrons Input SCFeefI eee eng ca 23 Digure 25 The cireunmsertptior fle D a ooo oa e ete haod A n snr a ae a 23 Figure 36 Circumscriptions 10 De Check ed oe edo de ld do 25 Figure 27 The circumsctipHon Input screech c eas iii 25 igure os The working note Meis 26 LEigure 59 The Workine name Input a a 27 Proure 40 The senerate Check names TED eine netos oi tt oe E REESE il 2 Fiseutre 41 The senerate check names Input SCEEOTE oi e eret entree iias 28 Pisiire 42 The cops classiticatton Te DU lea 29 Fipure 45 The copy classification THDUE SCIEN dui iia 29 Fisure 44 Tie Canned Queries MeN ds ias 30 Prone do The free lew MENU A en AMO uad n ben i bdo bonu IND 30 Lis re 46 The 1ree mamie displasia to 31 Bistro 47 Tres display Tie XU tutes sida 31 Figure 45 The TaxoVisu visualisation tl diia cia 33 Iu45ute 49 BackUp MMe A O 34 Fiere SELCA KUP WIN na 34 Bigure SH TT eontigurattopn Onasa EE tu e eed o t Pe
38. imens should be uniquely identified by a combination of herbarium collection number information or herbarium collector information However because taxonomic data can be very incomplete at specific stages of a revision if a specimen is entered with not enough information to distinguish it from another specimen a warning message is displayed that requests the confirmation of the operation Figure 21 A similar specimen was found in the database You can find it using the Find button in the edition window Are you sure you want to save the new specimen anyway Yes Ho Figure 21 Duplicate specimen warning message At the bottom of the input window a Find button is provided in order to allow the search of existing specimens in the database This avoids the input of duplicates When some information is provided and the Find button clicked the database will search all specimens satisfying the search criteria e g herbarium and collection number and display the results of the search in a new window as in Figure 12 PPS Change Existing specimens can be modified if necessary e g new information has been collected about the specimen In order to proceed to this edition the taxonomist must click on the Change Specimen button and select the specimen to be changed in the list of all available specimens When the changed have been made the modified specimen can be saved by clicking on the Save button or th
39. information The only compulsory piece of information is the reference information which can be the name of a journal or the complete publication information An abbreviation can be attached to the publication in order to produce reports See below Each publication description can contain a date which can be day month year month year or simply year and page information Page information should be a page number as specified in the ICBN but can also be a range of pages e g for the description of classifications Finally a set of authors can be selected for the publication In order to select more than one author the taxonomist needs to press the Control key on the keyboard and click with the mouse on all the authors that are required for the publication If new authors are required 1f they are not already described in the database the people edition window can be called by clicking on the Author button see section above When a new author has been described 1t will appear in the Author list to be selected Once all the available information has been input it can be saved by clicking on the Save button Because publication information is sometimes incomplete and require more research publications with similar values can be input in the database The new abbreviation window allows the description of a publication abbreviation Figure 16 The information that can be given is the abbreviation compulsory and the source of t
40. is a complex process and requires an important quantity of data In Prometheus all specimens can have a barcode top input box Although the ICBN does not support this technique of identifying specimens we believe that this is the only way to achieve complete accuracy and consistency of information Indeed if all specimens are identified by their barcode they can be uniquely identified whatever their use monographs publications publication of new names and the available data However this field is optional in Prometheus and can be ignored if the specimen to be input does not have a barcode as specimens at RBGE have All specimens in Prometheus have a list of collectors The names of all people defined in the database are displayed in a list left In order to choose a collector the taxonomist can highlight the collector then press the Add button at the right of the name list The selected collector will appear in the list on the right side of the window Collectors can be removed by selecting them in the list on the right and clicking on the Remove button The order of names in the list of selected collectors in important as this is the order top to bottom in which they will be displayed when the specimen is displayed If necessary it is possible to create new collectors by clicking on the Collector button This will bring the People input screen see section 2 3 All specimens can have a herbarium of origin In fact most specim
41. it For each object the information represented includes both the information contained by the object and the information it has been used for For example a type species will have publication author type and placement information but also information relative to which name it is the type Figure 46 This allows navigation within the database and discovery of properties of the data For example by opening a specimen it is possible to see which names it is the type of and which circumscription taxa it is in the circumscription of This shows overlaps between classifications By opening many tree view windows it is possible to compare entire classifications or compare the meaning of various names in different classifications ANALA Tree view Y Globba kerrii Craib Y Globba L Y Globba L 5 Glabha laeta K Larsen 5 Globba leucantha Mig Y Globba macrocarpa Gagnep 9 Glabba marantina L 5 Epithet marantina Y validly published true 5 Rank Species 5 Publication Carolus Linnaeus Mantissa plantarum 17715 170 5 Placement Globba L 5 Lectotype LINN Cat Linn herb 45 1 5 Author Carolus Linnaeus Y Inverse links 5 Lectotype of Marantella Horan 5 Lectotype of Glabba L 5 Lectotype of Globba L Y Globba nisbetiana Craib 5 Globba nuda k Larser 5 Globba obscura K Larsen Figure 46 The tree name display These templates can be found in the Prometheus root directory and are named ClassWrap
42. lay of the content of the database and the navigation though it the search of a group using its name the display of classifications as expandable trees the visualisation of the contents of the classification information contained within the database through Martin Graham s interface and the execution of queries Other modules can be written if necessary Each module is run when it is called on the command line after the action keyword E GUI 0 2 0 rev 53 04 10 00 File Taxa Dets Circumscriptions Descriptions Other Display Query Views Op Administrator Tree display Graph display I Debug qe Query cache Flush cache Ii Rules O Threaded rules 3 Threaded queries Index manager M Strong typing H And trick i Views Figure 52 The HTTP menu The HTTP server is driven by the HTML pages that are defined in the SERVER PAGES directory These pages can call action modules that perform complex tasks See the set of supplied pages for more information A FIAn 5 2 Text import Prometheus can import text data from other databases e g PANDORA Currently Prometheus can import specimen and classification information Figure 53 However other modules can be written in order to import other types of data A GUI 0 2 2 rev 55 31710700 File Taxa Dets Circumscriptions Descriptions Other Display Query Views Options Administrator Load specimens from text Export to XML Import from XML Export to HTML
43. lays the rank edition window see section 2 2 A publication can also be attached to the name as published names have publication information If the publication does not already exist it can be created by clicking on the Publication button that displays the publication edition window see section 2 4 In addition a series of authors can be connected to the name Authors are added by selecting the name of the author in the list bellow d Nair the publication list and clicking on the Add Auth button The name will appear in the list bellow Authors can be removed by selecting them in the selection list and clicking on the Remove button The order of authors in the selection list is important because only the first author is displayed when the name of the group is displayed All names should have type information Types represent a typical example of what a name is Type specimens and type taxa can be selected in the list at the top right of the window Then the kind of type must be selected in the combo beneath it and they are added by clicking on the Add button They then appear in the list bellow They can be removed from the list by selecting then in the selected list and clicking the Remove button The type of type is important as different types will have different effects on the database For example holotypes lectotypes and neotypes can be used when names are automatically derived by Prometheus whereas isotypes are i
44. might be for names Or a taxonomist might want to keep track of his decisions in the making of the revision by freezing his classifications at key stages AO PL 780m GUI 0 2 0 rev 53 04 10 00 File Taxa Dets Circumscriptic 1s Descriptions Other Display Query Views Options Administrator 7 Working Name Circumscription Generate Check Names Figure 42 The copy classification menu In order to support this iterative process Prometheus offers the ability to copy an entire classification and modify or expand it Figure 42 The choice of the classification to be copied is done in the copy classification screen Figure 43 The top left list contains the definition of all classifications As classifications are identified by an author and a publication the list of known classifications appears as a list of author publication pairs One of these must be selected and is the classification to be copied The bottom left list contains all known classifications and the list on the right side of the window contains all known authors In order to create a new classification a new pair publication author must be chosen Generally during the process of a revision publications are dummy publications that represent a stage in the process not actual publications For example such a publication could contain the name of the group being studied and the date at which the copy is made Once all the parameters are selected a click on the Copy
45. n this section how to describe in Prometheus existing published classifications Later these classification will be used in the process of a revision see section 3 2 1 General information on all windows All windows in Prometheus follow the same rules They all have New X Change X Save Delete and Cancel buttons where X is what is being edited These buttons are hereafter explained for each individual screen In all windows clicking on the cross at the top right of the title bar see Figure 1 closes the window without saving its contents The button at the left of that cross makes the window full screen and the button at the left of that button makes the window an icon zu Figure 1 Window buttons In addition on each window a help screen is available by clicking on the background of the window with the right button of the mouse or left if the buttons have been swapped and choosing help That help screen although simple should help understanding how Prometheus works When any window opens a message might appear giving a warning see Figure 2 This warning means that many concurrent accesses are open on the database Although this message is not a problem in itself it might show a problem in the database If the taxonomist chooses to open many windows at once which is allowed each window opened after the first one will display the message In that case it can be ignored As a general rule w
46. names has a taxonomist published what is the type of a nomenclatural taxon what are the names placed in a specific taxon what specimens two circumscription taxa share what specimens are not used in a particular classification 3 7 Visualising classifications When complete or partial classifications have been created it is important to be able to compare them This is particularly important for revisions that might gain insight by comparing revised classifications to previously published one Prometheus offers three main visualisation tools a tree display a set based display and a hierarchical display 3 7 1 Tree view The tree display is a very simple tree like display tool accessible from the Display menu Figure 45 ET 0 2 0 rev 53 04 10 00 File Taxa Dets Circumscriptions Descriptions Other I splay Query Views Options Administrator 7 Names TaxoWisu Circumscriptions Martin s visualisation All Figure 45 The tree view menu Certain kinds of elements in the database are displayed The elements to be displayed can be chosen using the predefined templates names only circumscriptions or everything The name only display shows only the nomenclatural information attached to names Figure 46 The circumscription display shows nomenclatural and circumscription information And the last display shows everything On each line of these displays a double click opens up the object displayed and gives more information about
47. nd 2 das IBI o teste teas 2 2 MD be c cH 2 2 5 TMU enn CE est EL IR LM LM MEC MU uL nM EE 22 23 2 CONN AIM M illa 25 2 8 3 Dr c E M Ha 22 S MAIS REL Me TUR TEE 23 Sb ACPO CUMS a PTOUD iioi nd ce eem e deat ttes scu ido oe aa cete pat ede a 23 3 1 1 boo dem M URS 24 SN EPA EI c MER RUE MURS 24 3 1395 BIO rom RETURN 23 23 Crains existe classicos uso A Ai 26 3 99 NOTE O AMES N s 26 34 TINGE d crop Merrill aa 27 3 9 COPY NME exis nP classrEICatlOfiS soda doe oo iecit inei eoo qb ute Duvet esa iii 28 30 Canned queres tad etos ied ied 29 Ile Nasualisme classtECatlOllse e x UU a pM ADU 30 Diels CSV LOW e o CE slserecais 30 301 2 yq E 3l Jla INDUTUETICT O 33 AUD RA 33 Communicator dl oo 34 Sele A AA ren ba e cce ssh eR s A cm Gunes nc es i cc LUE 34 D THU eorura tetra uiu idees o Red quan tutus rere Se re rT eae en utc oo sen 36 32 1 SPECIES Aia 36 3 2 2 CIaSSIHIC UOTIS sce errores PN De Ps Aia 36 SEE HB oo rr ERR 36 34 MIL MWnporte XDODUsusos teneo usen a RUE tas IS 37 A UU n 37 Table of figures Figure 1 RORIS LORS A O atte Daan he eee na ee 4 PEreure 2 Opening Ime SGA eC ee cece est f oben arabice awe Nt alton ota Mmi d se he utut O 5 Hisor Tool ins examples erre E 5 PU Tbe muse c soia tete hut AE EE LE ta
48. new Genus In that case Prometheus creates automatically the new combination from the available information and warns the user that the new name should be checked and published The created name is not marked as validly published until the user specifies it The calculation of names keeps the ascribed name and working name information supplied during previous stages of the revision F Naming groupings Basicalcaratae K Schum according ta Karl Moritz Schumann in Karl Moritz Schumann Dag Ceratanthera Horan according to Karl Moritz Schumann in Karl Moritz Schumann Das Pilas Globba albiflora Ridi according to Karl Moritz Schumann in Karl Moritz Schumann Das pm Globba bulbosa Gagnep according to Karl Moritz Schumann in Karl Moritz Schumann Dag Globba clarkei Baker according ta Karl Moritz Schumann in Karl Moritz Schumann Das Pile Globba L according ta Karl Moritz Schumann in Karl Moritz Schumann Das Pllanzenreich bs Globba L ascribed ta Marantella Horan according ta Karl Maritz Schumann in Karl Moritz Globba leucantha Mig according to Karl Moritz Schumann in Karl Moritz Schumann Das P Globba marantina L according to Karl Moritz Schumann in Karl Maritz Schumann Das Pila 4 _ Display all names c EFC Figure 41 The generate check names input screen 3 5 Copying existing classifications The process of a revision is iterative The taxonomist may try different configuration classifications in order to see what the results
49. on if the person to be deleted affects the display of names or specimens the message provides information on the repercussions of the action If the taxonomist confirms the deletion of the person all information related to that person is deleted Note that when people are deleted from the database the information they are used by e g specimen descriptions 1s not deleted Instead it simply loses the author or collector information EE Warning EJ gi The Guru s advice this operation may be dangerous People are used in many places Do you want to continue Yes Ho Figure 13 People deletion warning Edit People Hew Person Change Pers Surname Given Names Baker Brummit amp Powell 188771 CHA Yright Brummit amp Powell 1832 Craib Brummit amp Powell 1992 Abbrev Me DOB DOD Figure 14 The People input screen 2 4 Publication Publications in Prometheus are very important pieces of information They are used in order to describe nomenclatural taxa and to describe classification information see appropriate sections The window can be called from the Taxa menu Figure 15 ES GUI 0 2 0 rev 53 04 10 00 File axa Dets Circumscriptions Descriptions Other Display Query Views Options Administrator 7 Rank People Specimen Corrections Hame Figure 15 The publication menu 2 4 1 Input The description of a publication requires many different kinds of
50. ormation is not saved In order to create a new rank from this stage it is necessary to click on the New Rank button This will reset all input fields and allow the creation of the new rank 2 2 3 Delete If a rank is to be deleted it must first be selected using the Change button Once it is displayed in the ranks window clicking on the Delete button will erase all information related to this rank in the database Because ranks must be placed into a hierarchy of ranks when a rank that is not at either end of the hierarchy is deleted it is important to edit the previous and next rank so the chain of ranks is reconstructed Failure to do so might result in errors as some of the rules described in the ICBN will not be checked or will produce unexpected errors The deletion of rank information can be very dangerous for the consistency of the database Indeed because many rules of the ICBN rely on the existence of ranks and their order deleting a rank might lead to the failure of consistency rules or the detection of errors that do not exist If the taxonomist attempts to delete a rank from the database a message will remind him of the dangers of doing so see Figure 6 and if appropriate will explain why the deletion of the specific rank will have consequences for the consistency of the database If the taxonomist confirms his intention to delete the rank the rank will be deleted fey Warning m The Guru s advice this
51. pers txt They can be edited and changed if necessary These files contain the description of the database schema and the structure is as follows each class is described by its name and optionally by the name it must appear in the tree display For example in the extract of Figure 47 the Characters class should appear as DELTA character file Then each attribute of the class can be described and can also be displayed differently e g the attribute theTitle appears as Title In addition some attributes or classes can be hidden because they are not relevant to the current display For example the attribute calculatedToStringFullName in class Name should be hidden because it is internal data Hiding attributes or classes is done by adding a star in from of their name class Characters DELTA character file attribute theTitle Title class Name attribute theEpithet Epithet attribute theValidity Validly published attribute calculatedToStringFullName Full name attribute calculatedToStringFullNameNoAuthor Full name no author information Figure 47 Tree display file extract 3 7 2 TaxoVisu TaxoVisu is a more advanced visualisation mechanism Figure 48 TaxoVisu is designed to allow the comparison of classifications The TaxoVisu screen has 5 main parts Onthe left hand side a list of all the ranks that have been created is displayed On the right hand side a list of all names working names and specimens defined in the dat
52. r Display Query Views Options Administrator Init Load classification from text Load specimens from text Export to XML Import from XML Figure 54 Export to HTML The name of the generated file is Prometheus html 5 4 XML import export Prometheus uses XML as a means to transfer data between different databases Figure 55 GUI 0 2 2 rev 55 31 10 00 Taxa Dets Circumscriptions Descriptions Other Display Query Views Options Administrator Init Load classification from text Load specimens from text Import from XML Export to HTML Figure 55 Import Export XML When Prometheus is saved to an XML file the default file name is Prometheus xml No DTD has been defined for the format of XML files However this format is closely related to the Prometheus schema therefore it might not be useable by other systems without modification 6 References Greuter et al W Greuter J McNeill F R Barrie H M Burdet V Demoulin T S Filgueiras D H Nicholson P C Silva J E Skog P Trehane N J Turland D L Hawksworth International Code of Botanical Nomenclature Saint Louis Code Koelz Scientific Books K nigstein Germany Prom00 http www dcs napier ac uk prometheus PWK 00 M R Pullan M F Watson J B Kennedy C Raguenaud R Hyam The Prometheus Taxonomic Model a practical approach to representing multiple taxonomies Taxon Vol 49 Issue 1 pp 55 75 February 2000 2000
53. rently defined identified by their creation date Figure 50 When the OK button is clicked the selected backup is restored and the current state of the database deleted Select a backup to restore Thu Sep 28 14 57 05 GMT 2000 Wed Oct 04 08 43 38 GMT 2000 Wed Oct 04 10 43 34 GMT 2000 Wed Oct 04 10 49 09 GMT 2000 Thu Oct 05 13 08 46 GMT 2000 Med Oct 11 18 12 30 GMT 2000 Thu Oct 18 10 48 25 GMT 2000 Fri Oct 20 14 32 37 GMT 2000 Mon Oct 23 03 51 52 GMT 2000 Fri Oct 27 17 18 03 GMT 2000 Figure 50 Select backup window In order to delete a specific backup the user can click on the Delete backup option and select in the list the backup to be deleted Clicking on the OK button deleted the selected backup 5 Communication Prometheus is a system able to exchange data with other instances of the system with other database systems and with external users 5 1 HTTP server Prometheus has its own HTTP web server This allows external user to explore the database easily across the Internet The server is activated and deactivated in the Options menu Figure 52 When the checkbox is ticked the server is active and running By unchecking the box it can be deactivated and shut down Another check and it is re started In order to work properly the HTTP server must be set up A configuration file is given It is called http conf and can be found in the Prometheus Server HTTP directory see Figure 52 for an example T
54. s R O 35 Figure 2 Wie We He Bl siat ete RE rrr ates E edad 35 Prete 2955 Inpor ext iiss acces enc t dte Nen deii ness tcs o LE 36 Ercure 34EXportio MLM Pr c HRH 37 Er5 re 33 ImporUEXport ME dnce ERIT sates eii 27 1 Introduction The purpose of the Prometheus project is to create a taxonomic model and a database system supporting this model The aim of this new model and this new database system is the provision of a computing environment that allows taxonomists to work as they really do One very important limitation of most existing taxonomic models and database systems is the absence of support for multiple classifications These systems are limited by two flaws 1 they implement a model of taxonomy that does not allow the distinction of names from classifications which results in the inability to manage multiple classifications and provide automatic naming of taxa and 2 they are built on technology unable to handle the basic processes a taxonomist goes through while undergoing the description of a classification or a revision This document describes the Prometheus system from a user taxonomist point of view It is divided into two main parts the basic input of information and the imaginary scenario of a revision Through examples we will show how Prometheus can be used to support taxonomists work 2 Entering existing data As an example we will describe i
55. tM Sn ott 5 Figure 5 Duplicated data MESSI iS 6 Figure 6 Rank deletrOn Wang di 7 E15Ure 7 The pink mpl CEO odes iia 7 Picur S The peo ple Mentha xcs erates aue doe utei tiered cine Under ts cent em MN AU LI totaque ittis 8 Frsure 9 Duplicated person iniormation MO rea 8 FEieure TO INewcautbordbDre aora 9 Figure LT Adding source OF abbre VI AMON aye ues id nte eres danse us ii 9 Idpure 12 Seal Ci Te Sult AV ID dO V dira 9 Ligure I5 People deleton Warmin a ocu oe eost ee bet bene vete basate baee ben a p Lie sucede e buie Rude 10 Hisure 14 The People tpubseteelokseesadeas sth A i uk ee han bees tedcyannactas eu qutt adas 10 Fizu 155 Phe publication Me aia 11 Picure To Publication abbreviation Scripts 12 Faseure 17 Publication origini WIDOO Mi cad naea EEE E e EOE EE a EEA ii 12 Figure 18 Warning message for publication deletion seesseeseesesssssessessseseesessessrsersseseeseeseeseesesreseesesseseees 13 Fipute 19 The public amon Mpul SCLC CM vice odes eaten enr oett Sede 13 Broure 202 The aT e PEUT BULUM M 14 Figure 21 Duplicate specimen warning Message ccoccccnccoocconnnonnnonanonanonannnonnncnnnconncnncrnn nennen nne tne tnse nnne nne nnenns 15 Figure 22 Specimen deletion wating sli ida 15 Ligure 25 The Specimen mput SCEOeH s a tiet eite c e Opa b edet i itt cie ek aha ates 16 Pipu A Eos been tiet heo T nad ees it eai nd a ansa b tata eats 16 Pabute 25 Nomine Ulead alli 17 Fistre 20 C
56. ton A new window will appear Figure 12 that will display all persons whose surname is Linnaeus whatever their firstname and other details It is possible to search a combination of elements e g surname Linnaeus and firstname Carolus Tree view Root Node Ci Author Carolus Linnaeus Figure 12 Search result window 2 3 2 Change People descriptions can be changed by first selecting the person to be edited using the Change Person button The selected person then appears in the edition window Once the necessary changes have been made they can be saved by clicking on the Save button If the Cancel button is clicked or if the window is closed without saving the modifications will be lost In order to create a new person from this stage it is necessary to click on the New Person button This will reset all input fields and allow the creation of the new person 2 9 9 Delete People descriptions can be deleted from the database by selecting them using the Change Person button and selecting the person to be changed in the selection list and then clicking on the Delete button Because of their use in the display of information e g names deleting people might be very dangerous for the consistency of the information described in the database Therefore when the taxonomist requires the deletion of a person from the database a message reminds him of the danger of doing so Figure 13 In additi
57. w abbreviation see below The Clear button next to the Abbrev button unselects any selected abbreviation in the list Finally the date of birth DOB and date of death DOD can be described This information is optional As for all dates in Prometheus the DOB and DOD dates can be of many forms day month year month year or simply year If given the available data the new person already exists in the database an error message will appear and forbid the saving of data to the database see Figure 9 dm Creation error E This person already exists Figure 9 Duplicated person information error The new abbreviation window allows the description of an author abbreviation Figure 10 The information that can be given is the abbreviation compulsory and the source of the abbreviation optional If the source of the abbreviation is not already described in the database a new source can be added by clicking on the Origin button see below When the available information has been described it can be saved by clicking on the Save button An existing author abbreviation can be modified by clicking on the Change Abbreviation button and selecting the abbreviation to be changed Once the changes have been made they can be saved by clicking on the Save button An abbreviation can be deleted by selecting it first using the Change Abbreviation button and then clicking the Delete button Note that deleting
58. window A source of abbreviation can be changed by selecting it Change Database button and then saving it Save button It can also be deleted by selecting it and then deleting it Delete button The deletion of a source of abbreviation does not have consequences on the general functioning of the system FJ Edit Reference Database Hew Database Change Database Database Figure 17 Publication origin window 2 4 2 Change Publication descriptions can be changed by first selecting the publication to be edited using the Change Publication button The selected publication then appears in the edition window Once the necessary changes have been made they can be saved by clicking on the Save button If the Cancel button is clicked or if the window is closed without saving the modifications will be lost In order to create a new publication from this stage 1t is necessary to click on the New Publication button This will reset all input fields and allow the creation of the new publication 2 4 3 Delete Publication descriptions can be deleted from the database by selecting them using the Change Publication button and selecting the publication to be changed in the selection list and then clicking on the Delete button Because publications play a very important role in the workings of Prometheus e g they identify classifications and participate in the definition of names
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