Litchi 2.20 User Guide - Pages supplied by users
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1. Test CSV import 29 07 04 M 9 07 04 ctcececz 100 Complete Rules were run successfully but no 16 54 17 05 C8 relationships were found Browse Delete DA af J p LESE Buser gue vz 2 Blinaomiegollum INBOX ximiar Let 2 2 Mozil JEuilder 9 hon i 5 1 5 1 B D EM s J 1 B 1 LS c page 9 of 22 Litchi User Guide v 2 20 24 01 2006 Litchi2 2 Mozilla a Eile Edit View Go Bookmarks Tools Window Help m Q Q Q Q amp http grab biol soton ac uk 8080 litchi22 F rontServlet action 4 amp Home EjBookmarks DS Liteni 2 2 a Import List Delete A List Run Rules Browse Name Relations Browse Cross Maps Manage Rules Manage Users Logout Import Monitor Please select which running of the rules you wish to view Refresh First List Second List Time of Run ae Run Status CSV authors 1 29 07 04 CSV authors 2 29 07 04 29 07 04 C1 C2 C3 C4 C5 C6 o 1741 17 11 17 44 C7 C68 62 5 Complete Running rule C6 ILDIS acacias 29 07 04 29 07 04 C4 C5 C6 100 Complete Rules were run successfully with 39 16 28 17 08 relationship s found Browse Delete Test CSV import Another CSV 29 07 04 29 07 04 T TA T10 T9 100 Complete Rules were run successfully with 12 29 07 04 16 54 17 07 17 07 relationship s found Browse Delete ILDIS acacias 29 07 04 Test CSV import 29 07 04 T TA T10 T9 100 Complete2. nd CSV authors 2 29 07 04 17 11 XML format lt Previous Taxon Next Taxon gt Search For Taxon Related Taxa in CSV authors 2 CONGRUENT Add Relationship With New Taxon Campanula forsythii A amp rcang Podlech accepted Make Current Taxon congruent Change Relationship Remove Relationship OF iavascript searchPopUp t l search CERE git piu i Buser guide v ainaomie oon INBOX xin ncn 22 M ct 22 m ueuizer9 1 Lo Lo La WAICic Lo La LS lt c The results of the search will be displayed in the pop up window and to select one you should click the Make Current Taxon button The pop up window will disappear and you will be returned to the cross map display with that taxon at the top and its related taxa below page 16 of 22 Litchi User Guide v 2 20 24 01 2006 Litchi 2 2 Mozilla Litchi 2 2 Mozilla eji E Search Results m Chamaecytisus austriacus Linn Link Make Current Taxon accepted a prp ier r promi t id dicet S abs dul le Relations Browse Cross Maps Manage Rules Manage Users Logout nd CSV authors 2 29 07 04 17 11 XML format Back to Search Close Window lt Previous Taxon Next Taxon gt Search For Taxon Related Taxa in CSV authors 2 Add Relationship With New Taxon CONGRUENT Campanula forsythii Arcang Podlech accepte Make Current Taxon con
3. Both of the options require the List Name field to be completed you should enter a uniquely recognisable name for the list Once the import has started you will be redirected to the Import Monitor screen so that you can see the progress of the import see next section page 5 of 22 Litchi User Guide v 2 20 24 01 2006 4 Import Monitor This page allows you to see the status of recent imports To see the latest status you need to click the Refresh Status link Note that a list will only be available to the rest of the Litchi system once its import is complete Litchi 2 2 Mozilla Six a Eile Edit View Go Bookmarks Tools Window Help Q Q Q Q Sc hitp grab hiol soton ac uk 8080 litchizz FrontServlet action importMonitor 4 Home Bookmarks ALS Litchi 2 2 E Import List Delete A List Run Rules Browse Name Relations Browse Cross Maps Manage Rules Manage Users Logout Import Monitor Import status Refresh Status List Name Import Started Gathering Info Importing list Information ILDIS acacias 29 Jul 2004 16 28 19 100 75 Performing import Clear Failed Imports OF a J LEGES oo eee O E anna Ws EI page 6 of 22 Litchi User Guide v 2 20 24 01 2006 5 Deleting a List This page presents you with a table of the available lists i e only those which have finished being imported along with the name of the user who imported th
4. Rules were run successfully but no 16 28 29 07 04 16 54 17 05 relationships were found Browse Delete Test CSV import 29 07 04 100 Complete Rules were run successfully but no 29 07 04 16 54 i 17 05 C1C2C3C7C8 lrelationships were found eris rbslel Eg 7 eT oe o eee E O o ST ARA AERE o To see the latest status simply click the Refresh link at the top ofthe page page 10 of 22 Litchi User Guide v 2 20 24 01 2006 Once the run has completed you can view its results by clicking the Browse button at the end ofthe row You will then be presented with the relationships found If there were none then an informative message will be shown at the top of the screen However if relations were found then they will be displayed in alphabetical order by accepted taxon The related taxon pairs are shown side by side with the names that were found by a rule highlighted in red The class name ofthe rule that has been broken is displayed to the side of the names The figure below shows an example of running the rules between two lists Litchi 2 2 Mozilla a File Edit View Go Bookmarks Tools Window Help Q Q Q I http Xm biol soton ac uk 808U litchiz2 F rontServlet action browseRelations a 4i Home EjBookmarks Q Litchi 2 2 Import List Delete A List Run Rules Browse Name Relations Browse Cross Maps Manage Rules Manage Users Logout Import Monitor Displaying the relationships
5. guada docs Binaomieg ironena gaeox x lucri 22 grueuiero i LA La La Ea Lo LE 3 2 p page 2 of 22 Litchi User Guide v 2 20 24 01 2006 These features are Import List Import a snapshot of a GSD or regional database called a list Import Monitor View the current status of lists that are being or have been imported into Litchi Delete A List Delete an existing imported list Run Rules Running some rules against one or two lists Browse Name Relations Browse the name relations that have been found from previous rule runs and generate a cross map from them Browse Cross Maps Browse the cross maps that have already generated Manage Rules View the rules in the system links to delete amp upload new rules Manage Users Manage the Litchi users allows creation updating amp deletion of users Logout Logout of Litchi Note that the links you can see on the tool bar will be limited by the permission level you have The possible permission levels are Read Read only access to the rules relations and cross maps i e they cannot import lists or run rules Write Read plus the ability to import delete lists run rules generate and edit cross maps and to delete rule runs Rules Write plus permission to delete and add new rules Administrator Rules plus permission to add update and delete Litchi users Therefore only the highest level users can see all ofthe features listed her
6. password twice to ensure it was correctly entered page 21 of 22 Litchi User Guide v 2 20 24 01 2006 Litchi 2 2 Mozilla jak a Eile Edit View Go Bookmarks Tools Window Help Q Q Q Q amp http grab biol soton ac uk G080 litchi22 F rontServlet action manageUsers amp for edit a i ie a be a Home Bookmarks ALS Litchi 2 2 a Import List Delete A List Run Rules Browse Name Relations Browse Cross Maps Manage Rules Manage Users Logout Import Monitor Username richard n Re enter Password fr Permission Level Frule Update User OF Done Esme E ESI Buser udev a uen Docs MBinaomi gral INBOX Xim BLitchi 2 2 M Deutera 1 1 La Lo Lo Bic LA La LS A OD E At the bottom ofthe screen there is a link to create a new user which is a very similar screen to when editing an existing user You cannot create a user whose name already exists in the database After any edit create or delete you will be returned to the initial listing of users to see the affect of your changes Note that only users with the highest permission level Administrator will be able to access this area 12 Logging Out This will end the session and you will have to login again to access the system If an import was in progress then it will continue after you have logged out page 22 of 22
7. 80 litchi22 FrontServlet action getCrossMapRuns m 4 amp Home EjBookmarks amp Litchi 2 2 Import List Delete A List Run Rules Browse Name Relations Browse Cross Maps Manage Rules Manage Users Logout Import Monitor Please select which cross map you wish to view First List j Second List Time of Calculation Test CSV import 29 07 04 16 54 Another CSV 29 07 04 17 07 29 07 04 17 26 Browse csv authors 1 29 07 04 17 11 csv authors 2 29 07 04 17 11 29 07 04 17 20 Browse EJ ora ESEE Bs Ed i Euser oue v22 Bnaomi gollum G2INBOX Ximian Euni 2 2 Mozil eunero hon 4 Lo Lo La ER 1 Lo La Lo 5 e 2 AS Clicking on the Browse button next to the cross map you wish to view will take you to the screen for that cross map page 14 of 22 Litchi User Guide v 2 20 24 01 2006 The first taxon alphabetically from the first list of the cross map will be displayed with its related taxa if there are any below From here you can navigate through the first list by using the Previous Taxon and Next Taxon buttons You can also search within the list for a particular taxon by clicking on the Search For Taxon link Litchi 2 2 Mozilla ak a Eile Edit View Go Bookmarks Tools Window Help Q Q Q Q S http grab biol soton ac uk6080 itchiza FrantServiet action browseCrossMap a 4 Home Bookmarks Import List Delete A
8. List Run Rules Browse Name Relations Browse Cross Maps Manage Rules Manage Users Logout Import Monitor Displaying the cross map between CSV authors 1 29 07 04 17 11 and CSV authors 2 29 07 04 17 11 XML format Current Taxon in CSV authors 1 Campanula forsythii Podl accepted Previous Taxon Next Taxon gt Search For Taxon Related Taxa in CSV authors 2 Add Relationship With New Taxon CONGRUENT Campanula forsythii Arcang Podlech accepted _Make Current Taxon congruent z Change Relationship Remove Relationship DA af J P Z o oen oy SRST ETT RRS page 15 of 22 Litchi User Guide v 2 20 24 01 2006 The taxon search link will pop up a window for you to enter a genus epithet specific or infra or binomial into and then it will display the taxa that matched if the were any This search is not case sensitive and does not require wild cards as it automatically puts them at the start and at the end of your search string For example if you were looking for the taxon Chamaecytisus austriacus you could simply enter aust and your taxon would match However the fewer letters you enter the more likely it is that there will be multiple matching taxa found Litchi 2 2 Mozilla Litchi 2 2 Mozilla eji E Please enter genus epithet or binomial to search for pindi Find Taxon Close Window le Relations Browse Cross Maps Manage Rules Manage Users Logout
9. Litchi 2 20 User Guide Litchi 2 2 Login Mozilla Richard White amp Naomi Russell 24 January 2006 a Eile Edit View Go Bookmarks Tools Window Help Q Q Q Q Q http grab biol soton ac uk 80B0 litchiz2 login jsp liti aN ili a 4 amp Home EjBookmarks W amp Litchi 2 2 Login x Litchi 2 2 29 07 2004 Username Password Login Oy Done E e i Euser auae AE ef 3 docs Binaomi g home nat QiNsox x iluicn 2 21 ueuitero LS Lo LA Bach n wy ES E c Contents PM nois 2 2 Access th SVSLODILu see po podafedo nobia ded RR I ur Apa Aa EEE epus VP MK NN OA M OUI MM ME 2 3 Impor ng a List E 4 4 Import MOonBIDBE iod oreari NNI ea ERR MURDER cd rh R EM A E ENEKO pn Rd 6 35 D l ting DAE 7 6 RUNNING th RUSS T H 8 Te Browse Nam Relations scddictnsaiccsdasiutasiadectstaciaanecuorubashascdauesehsisbnateduniactascaniies deudidaareacauissa 9 Be JProducis Gross MOAp ose onividar eritis kb i bd rna aE E EREA SONER REER EES Plau 13 9 Browsing the Generated Cross MapSs sssesesseessssesesesssssteesesestsssteesssstesesestessseeeseseeets 14 10 Managing BAlespsespiscont ii ded aaeeea albas a nA NA EA E RR CER NU a E UNUS RE 19 He Cur uud cM mee I 21 L2 Lossino OUt desinet or GS HR VIR Meets ap AREA EEE AEE EA REA EA OR OR EREE ca dE 22 page of 22 Litch
10. between two lists CSV authors 1 29 07 04 17 11 amp CSV authors 2 29 07 04 17 11 run at 29 07 04 17 11 Reverse View Cross Map Campanula forsythii Podl accepted C5 100 C5 100 Campanula forsythii Arcang Podlech accepted Chamaecytisus austriacus Linn Link accepted C1 67 C5 99 Fed austriacus L cie duni Cytisus pindicola Hal csy sy nym C6 102 C6 102 Cuscata arvensis Beyr ex Engelm accepted C2 87 C2 87 Cuscata arvensis Beyrich accepted ped felted Ball Desine bes e usd C1 uo CIO REED biflorus Desf Frodin amp hia accepted ie c2 Ai 72 Done i a E i J Buser gude v22 raomie gotum 2080x xine ilic 2 2 Mozil JBuilder 9 hon j Lo Lo L2 Ea LO Lo Lo fe If a taxon is involved in more than one rule break with more than one taxon then the related taxa are listed on the right hand side To distinguish which name is related to which other name each relation has its own unique number which is also shown in parentheses after the rule class name so when a taxon has multiple rule breaks each rule breaking name pair can easily be differentiated For two list runs the default view presented is from that ofthe first list that was imported into the database That means any taxon in the first list that is involved in rule breaks no matter how many is only listed once on the left hand side The related taxa from the second list are l
11. ccepted congruent au Link Add Relationship synony Cytisus pindicola Hal synonym le Relations Browse Cross Maps Manage Rules Manage Users Logout nd CSV authors 2 29 07 04 17 11 XML format Back to Search Close Window lt Previous Taxon Next Taxon gt Search For Taxon Related Taxa in CSV authors 2 Add Relationship With New on CONGRUENT Campanula forsythii Arcang Podlech accepte Make Current Taxon congruent _Change Relationship p ym 9 ped Remove Relationship Of isvascript searchPopUp 1 678 1 add es TY TEEEETECEEETCTTNT TEE O pri ri ri ria If you would like to see the complete cross map in XML format simply click the XML format button in the top right hand corner ofthe screen This will give you the raw XML cross map To retum to Litchi simply click the Back button in your browser page 18 of 22 Litchi User Guide v 2 20 24 01 2006 10 Managing Rules This page displays all the rules that are currently in the system including their name description class name and priority The class name is how the rules are referred to in the relations display Litchi 2 2 Mozilla ak a Eile Edit View Go Bookmarks Tools Window Help Q Q Q Q amp http grab biol soton ac uk 8080 litchi22 FrontServlet action getRules amp fo
12. e Obviously before running any rules against a list you need to import a list and upload some rules page 3 of 22 Litchi User Guide v 2 20 24 01 2006 3 Importing a List To import a list click on Import List on the tool bar You will then be presented with this page that has two ways to import information into the system Litchi 2 2 Mozilla a File Edit View Go Bookmarks Tools Window Help Q Q Q Q S http grah hiol soton ac uk BD80 litchi22 FrontServlet action importList i l n a 4 amp Home Bookmarks afeumzz 1 5 Import List Delete A List Run Rules Browse Name Relations Browse Cross Maps Manage Rules Manage Users Logout Import Monitor Please enter the details of the GSD List to import Choose a Wrapper URL http jotun cs cf ac uk 8080 ILDIS1_2 WRAPPER zj Or Specify a URL gt Search String Bois List Name LDiS acacias Import OR CSV File Location Browse List Name aa Description 4 Import Oy Done ESE ELEM Euser ute v BD docs iinconiegol INBOX xm Bilucni22 w JBuilder 9 A j lt LA Lo La gt joe LA La 7 B E The first is to connect to a GSD through its wrapper to obtain taxon information that corresponds to the Common Data Model CDM 1 2 requests The most important part of this is the URL If this is not correct then the system will not be able to locate the GSD You can either select a URL from the drop dow
13. em and the date and time of import It is important to note that deleting a list is not reversible and will also delete all results from running the rules and any cross maps that the list was involved in Litchi 2 2 Mozilla N ox File Edit View Go Bookmarks Tools Window Help Q Q Q Q amp http grab bioL soton ac uk 6080 litchiz2 FrontServlet action getLists amp for delete mM 4 Home E3Bookmarks 2 Al S Litchi 2 2 a mport List Delete A List Run Rules Browse Name Relations Browse Cross Maps Manage Rules Manage Users Logout mport Monitor Please select the list you wish to permanently delete List Name Imported By Date Imported ILDIS acacias naomi 29 07 04 16 28 Delete Test CSV import naomi 29 07 04 16 54 Delete LL er cag y 495 EE i user guide v2 2 Binaomi gollum G2 INBOX Ximiar gif itchi 2 2 Mozil JBuilder 9 hor NK x Lo Ea Lo 7 LA A page 7 of 22 Litchi User Guide v 2 20 24 01 2006 6 Running the Rules Click on the Run Rules link in the tool bar You will be presented with a choice of lists and rules If no lists or rules could be found then a message will be shown informing you that you need to import a list or upload some rules Litchi 2 2 Mozilla x GNX a Eile Edit View Go Bookmarks Tools Window Help Q Q Q Q S http grab biol soton ac uk 8080 litchi22 FrontServlet action getRules amp for run a 4i H
14. gruent v Change Relationship P 9 I pted Remove Relationship Of iavascript searchPopUlp t T search SP pi 4S 4 Buser oue v naomi goll G2INBOX Ximi Buni 22 M iucniz2 JBuilder 9 A La Lo Lo e LA L2 Lo a e To look at the cross map from the view of the second list you should click on the Make Current Taxon button for one ofthe related taxa This will swap the current taxon for this one and change the view to be looking from the other list s perspective If you have permission i e higher than read only you will also be able to edit the cross map You can remove a relationship by clicking the Remove Relationship button or change its type by selecting a different relationship from the drop down menu below the current relationship and clicking the Change Relationship button You can also add new relationships by clicking the Add Relationship With New Taxon link This link will pop up a taxon search window just like the earlier pop up window which allows you to search for a taxon to relate to Alongside the search results is a drop down for you to select the type of new relationship and clicking the Add Relationship button will add the relationship and then close the pop up taking you back to an updated view of the taxon relationships page 17 of 22 Litchi User Guide v 2 20 24 01 2006 Litchi 2 2 Mozilla Litchi 2 2 Mozilla Search Results Cytisus austriacus L a
15. i User Guide v 2 20 24 01 2006 1 Introduction Litchi 2 is a web based system to aid in the checking of taxonomic lists for integrity and also to deduce the taxon relationships between taxa in two lists called a cross map 2 Accessing the System The main Litchi web page can be found at http biodiversity cs cf ac uk litchi Click on the link to the latest version ofthe Litchi system 2 20 at the time of writing and you will be presented with the log on screen above Note You can also go straight to http biodiversity cs cf ac uk 8080 litchi2 but this URL is not guaranteed to remain available as it will vary as version numbers and deployment details change To access the system you will need a valid username and password which you should enter and then click the Login button or simply press the Return key Once you have logged on you will see a tool bar across the top ofthe screen It is this tool bar that gives you access to the system s features Litchi 2 2 Mozilla Eile Edit View Go Bookmarks Tools Window Help Q Q Q Q S http grah hiol soton ac uk BD80 litchi22 FrontServlet action login a 4 amp Home Bookmarks amp Litchi 2 2 Lj Import List Delete A List Run Rules Browse Name Relations Browse Cross Maps Manage Rules Import Monitor Manage Users Logout Welcome naomi Please select an option from the toolbar above O4 Done EE EE Buser
16. isted on the right hand side next to the first list taxon Therefore taxa from the second list may be listed more than once depending on how many rule breaks they are involved in To reverse this view and have the second list s taxa listed once with their related taxa displayed to the page 11 of 22 Litchi User Guide v 2 20 24 01 2006 left click on the Reverse View button This button will not be present when the relations shown are on a single list Two list rule runs will also have a Cross Map button which will allow the generation ofa cross map from those relations see the next section For rule runs on a single list if a taxon conflicts with itself it will be highlighted in yellow so that it can be easily identified as a taxon conflicting with itself and not simply a repeated one The figure below shows an example of this Litchi 2 2 Mozilla N a Eile Edit View Go Bookmarks Tools Window Help on ac uk 8080 litchi22 FrontServlet action browseRelations Al amp Litchi 2 2 Import List Delete A List Run Rules Browse Name Relations Browse Cross Maps Manage Rules Manage Users Logout Import Monitor Displaying the conflicts for a single list World CSV 29 07 04 17 15 run at 29 07 04 17 15 Chamaesyce canescens L Prokh subsp canescens C7 105 C8 107 Chamaesyce canescens L accepted C8 107 f T L Moer C7 105 Euphorbia canescens L synonym Euphorbia pinn
17. lected are displayed in the order in which they have been or will be run which is determined by their priority The status ofthe run tells you which rule the run is up to and whether any errors have occurred You will not be able to browse or delete a rule run until it is complete Also you will only be allowed to delete a rule run once it is complete and if you have the required permission level Litchi 2 2 Mozilla NEN a File Edit View Go Bookmarks Tools Window Help Q Q Q Q amp y http grab biol soton ac uk 8080 litchi22 FrontServlet action getRulesExecutians iv I lal j T 5 4 Home Bookmarks S Litchi 2 2 o Import List Delete A List Run Rules Browse Name Relations Browse Cross Maps Manage Rules Manage Users Logout Import Monitor Please select which running of the rules you wish to view Refresh Rules First List Second List Time of Run Executed Run Status in order ILDIS acacias 29 07 04 i Weert leres eee Sa nisin p 16 28 i 17 08 C4 C5 C6 psum Complete Running rule C5 Test CSV import 29 07 04 Another CSV 29 07 04 29 07 04 T TA T40 T9 100 Complete Rules were run successfully with 12 16 54 17 07 17 07 relationship s found Browse Delete ILDIS acacias 29 07 04 Test CSV import 29 07 04 29 07 04 T TA T40 T9 100 Complete Rules were run successfully but no 16 28 16 54 17 05 relationships were found Browse Delete
18. n list or enter a new one in the text field Or Specify a URL Anything entered into this text field will take priority over the URL selected from the drop down list The Search String allows you to restrict your search to taxa with certain names The character is wild that is it will match anything For example searching for Acacia gives accepted names from other genera that have Acacia names in synonymy So the search string can be used to restrict the import to a certain genus of interest The search is not case sensitive so Acacia is the same as searching for acacia page 4 of 22 Litchi User Guide v 2 20 24 01 2006 The second option is to upload a Comma Separated Values CSV file containing taxon information in the format lt genus gt lt specific epithet gt lt specific authority gt lt status gt lt infra epithet gt lt infra authority gt The infra epithet and authority are optional There should be no spaces around between the fields and their separating commas Ifa field contains a comma then it must be quoted with double quotes This format is a standard way of exporting data from Excel so it may be easiest to enter the data into the spreadsheet and export it in CSV format The taxon should be separated by lines beginning with a dash To upload a file you should use the Browse button to locate the file in your file system An optional description can be entered
19. nage Rules Manage Users Logout Import Monitor Please enter the values to be used in the generation of the taxon relationships for the cross map The factor to divide by when only the latin components of a name match Bo The factor to divide by when the names are connected through an epithet and basionym authority 20 The factor to increase the misapplied name relationships by po The minimum confidence that we will allow for calculations pz The maximum allowed difference between confidences used to calculate higher relationships p3 Generate Cross map 94 bo xu ne Ln xo ESI Euser guae v2 2 Bnaomi gollum I PONBOX ximiar Butchi 2 2 Modi Builders mon j L2 Lo Lo EM sc Lo LA La 4 r2 Clicking on the Generate Cross map button will calculate the cross map from the relationships using the factors you have entered You will then be presented with the cross map display which is covered in the Browsing the Generated Cross Maps section For more information about the cross map and how it is calculated see the document Cross map Rules page 13 of 22 Litchi User Guide v 2 20 24 01 2006 9 Browsing the Generated Cross Maps From the tool bar click Browse Cross Maps and you will be presented with a list of cross maps that have already been generated as shown in the figure below SLitchi2 2 Mozilla Eile Edit View Go Bookmarks Tools Window Help Q Q Q Q Q http grab biol soton ac uk 80
20. ome EjBookmarks amp Litchi 2 2 Import List Delete A List Run Rules Browse Name Relations Browse Cross Maps Manage Rules Manage Users Logout Import Monitor Please select one or two lists and the rules you wish to run against them Test CSV import ETE LEE Accepted amp Synonym non pp Accepted Names Synonym matches non pp Acc Name amp Synonym Same Latin Different Authorities Acc Names Same Latin Different Authorities Synonyms Same Latin Different Authorities Matching Full Name Matching Latin Components Autonym B Species authors don t match Run Rules er x E 7 p Eg A guide v2 2 Blinaomi amp gollum l INBOX Ximiar fitch 2 2 Mozil JBuilder9 hon a Lo Lo BV ER 2 Lo rz Log vi M i b Select one or two lists and at least one rule and then click the Run Rules button You will then be directed to the Browse Relations screen see next section to follow the progress of your rule run page 8 of 22 Litchi User Guide v 2 20 24 01 2006 T Browse Name Relations You can also get to this page in two ways either via the Browse Name Relations in the tool bar or from running the rules You will be presented with a table of all the rule runs including those which are still in progress with the most recent run at the top They are listed by list name s time the rules were run which rules were selected for that run and the status ofthe run The rules se
21. r browse Im a 4i Home Bookmarks W S Litchi 2 2 Ix mport List Delete A List Run Rules Browse Name Relations Browse Cross Maps Manage Rules Manage Users Logout mport Monitor These are the rules that currently imported into the Litchi system Rule Name Description lass Priority Name Accepted amp Synonym non pp A full name which is not pro parte cannot appear both as an accepted name and a synonym C1 1 Delete Accepted Names A full name cannot appear more than once as an accepted name C2 1 Delete Synonym matches non pp A full name which is not a pro parte name cannot be a synonym of more than one taxon C3 1 Delete Acc Name amp Synonym Same Latin A full name with the same Latin components but different authorities which is not a homonym or ca 1 DE Different Authorities misapplied name cannot appear both as an accepted name and as a synonym Acc Names Same Latin Different A full name with the same Latin components but different authorities which is not a homonym cannot C5 4 S Authorities appear as an accepted name of different taxa Synonyms Same Latin Different A full name with the same Latin components but different authorities which is not a homonym or in A a C6 1 Delete Authorities misapplied name cannot appear more than once as a synonym Matching Full Name Finds matching full names between two lists T1 1 Delete Matching Latin Components Finds matching latin components of names between two lists T4 1 Dele
22. s the Litchi class org sp2000europa litchi2 rules Rule An overview of how to write new rules is contained within the Developer s Guide document page 19 of 22 Litchi User Guide v 2 20 Eile Edit View Go Bookmarks Tools Window Help 99909 a 4 amp Home EjBookmarks s amp Litchi 2 2 amp hittp grab biol soton ac uk BO80 litchiZ2 rule_upload jsp Import List Delete A List Run Rules Browse Name Relations Browse Cross Maps Import Monitor Manage Rules Manage Users Logout Please enter the location of the new rule to be uploaded Rule Class Location Upload OF bone Jf D LT 3 INN ESPE H d user guide v 3 Litchi Docs ifnaomi grall G2INBOX Xim lfLitchi 2 2 M Dieuiers 1 4 La Lo Lo ER Ci LA La La o E This page will only accept files if they are of type class i e have a class extension It will also not accept files that have the same name as an existing rule If any such conditions are detected or if any errors occur while the rule is being uploaded you will be informed and asked to try again Note that while any user can browse the rules only users with a certain level of permissions Administrator and Rules levels can delete and upload rules page 20 of 22 24 01 2006 Litchi User Guide v 2 20 24 01 2006 11 Managing Users Clicking on this link takes you to a listing of all the users that currently have access to the Li
23. tchi system along with their permission level Each user can be deleted or updated from this screen Litchi 2 2 Mozilla NN a Eile Edit View Go Bookmarks Tools Window Help Q Q Q Q S hitpz grab biol soton ac uk 8080 litchiz2 FrontServlet action manageUsers amp for list p I a u 4 amp Home Bookmarks amp Litchi 2 2 mport List Delete A List Run Rules Browse Name Relations Browse Cross Maps Manage Rules Manage Users Logout mport Monitor These are the users who are currently in the system Username Permission Level naomi fadmin Read and write permission permission to edit rules and to edit users esit Delete richard ladmin Read and write permission permission to edit rules and to edit users _eait Delete john admin Read and write permission permission to edit rules and to edit users Edit Delete judith jadmin Read and write permission permission to edit rules and to edit users Edit Delete frank ladmin Read and write permission permission to edit rules and to edit users Edit Delete Create A New User oT 24 ESEE p im i Euser ouide va Len pocs M Binaomi gral G2INBOX Xim EfLichi 2 2 M Pruner i 4 Lo Lo Lo ER 1 Lo La Lo 5 e When deleting a user you cannot delete yourself This is simply to ensure that at least one user is always present in the system EJ When editing a user s information you must enter the
24. te Autonym amp Species authors don t i LL sors and ite a match Finds an autonym and its matching species between two lists whose authorities do not match T10 2 Delete Autonym amp Species authors match Finds an autonym and its matching species between two lists whose authorities match T9 le Delete i The species epithet and the authority of a full name in one taxon cannot be the same as the species parody B Basan epithet and basionym authority of a full name in another taxon 67 P gend iti The species epithet and basionym authority of a name cannot be the same as the species epithet and pa Authorities basionym authority of another name either in the same or in a distinct taxon cs P Fatis Upload A New Rule D 93 ESFE E i Euser ouae v a Litchi Docs Bfinaomi gral G2INBOX Xim Lichi 2 2 M Deutera 1 1 Lo La Lo EAM Cic Lo La LS ac Each rule can be deleted from this page by pressing the Delete button alongside the rule Deleting a rule permanently removes the rule class file from the underlying file system and removes any references to that rule from the database Therefore any relationships that were found by this rule will also be deleted There is a link at the bottom of this page which takes you to the Rule Upload screen This allows you to introduce a new rule into the Litchi system by uploading a file from their local system The new rule must be a Java class file that extend
25. ulosa Loj ac synony m Euphorbia amygdaloides L accepted C7 106 Euphorbia amygdaloides L subsp amygdaloides accepted Tithymalus amygdaloides L Hill synonym Euphorbia orjeni Beck synonym Euphorbia sylvatica Jacq synony i orbi i2 Timb Lagl Euphorbia falcata L subsp macrostegia Bornm O Schwarz C4 104 Euphorbia falcata L subsp macrostegia Bornm O Schwarz accepted accepted OR 104 Euphorbia falcata L var macrostegia Bomm synonym me A on wy Buser gude v22 Bllnaomi amp gollum I 2 INBOX Ximiar gilutchi 2 2 Mozil ueunaers nor y BY BY pF Lo BY Lo e page 12 of 22 Litchi User Guide v 2 20 24 01 2006 8 Producing a Cross Map To produce a cross map you must first run some rules between two lists and then browse those relations For the cross map to produce the best results it is recommended that the user run only rules T1 T4 C7 and C8 Click the Cross Map button at the top ofthe page and you will be presented with a page of the various factors Litchi uses to calculate the cross map so that you can alter them as required Litchi 2 2 Mozilla ak Eile Edit View Go Bookmarks Tools Window Help Q Q Q Q amp http grab biol soton ac uk 8080 litchiZ2 map factors jsp al i a 2 a 4 Home EjBookmarks amp Litchi 2 2 EJ Import List Delete A List Run Rules Browse Name Relations Browse Cross Maps Ma
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