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VBv2 0_user_manual - AIMS

1. Kigropiast tr Amiloplast tr LJ Plasbdler tr H cre ekirde i tr Nukleus lr Cekrdek tr term edit term edit term edi term edit term edit term edit termedi term create Action User Yasemn Cevik Yasemn Cevik Yasemn evik Yasemn Gevik Yasemin Cevik Yasemin Cevik Yasemin Cevik Yasemin Cevik 21 03 2014 11 M 15 21 03 2014 11 00 42 21 03 2014 11 00 31 21 03 2014 11 00 21 21 03 2014 11 00 03 21 03 2014 10 59 50 21 03 2014 10 59 39 21 03 2014 10 59 22 Filters may be used to reduce the number of actions shown Click the Apply filter option in the top right corner of the Recent changes module Error Reference source not found The following specific filter options Figure 46 facilitate the search for recent changes e Filter by user By default all registered users are unselected To view changes by specific users simply check the check box in front of their name To select all users check the All box at the bottom of the list to uncheck all users check the All box again Note These settings will be saved also for next sessions e Filter by action By default all possible actions are unselected To select actions simply check the appropriate check boxes Note These settings will be saved also for next sessions VB 2 0 User Manual Page 52 of 101 e Filter by date By default all changes are shown since the set up of the VB installation y
2. e Starts with With this option you will retrieve the concepts labelled by terms in the languages you selected that start with the search string typed in This search also retrieves composed terms that contain words starting with the string typed in Example In Figure 27 you can see the results of a search for tomato VB 2 0 User Manual Page 34 of 101 Signed in as Administrator Administrator to Agrovoc indexed v Administration About VocBench v A RSSfeed Preferences Help VERSION 1 3 DEVELOPMENT Voc Be nc h Stars win Y tomato Advanced search Last results i Recent changes Relationships Validation Export Statistics Concept navigation history Co Search results Concept Last update date Cherry tomatoes en 24 02 2009 09 46 20 Cyphomandra betacea en Tree tomato en 16 07 2009 09 23 32 Lycopersicon esculentum en Lycopersicon lycopersicum en Solanum lycopersicum en tomato plant en 23 04 2010 04 21 29 Tomato mosaic tobamovirus en Tomato mosaic virus en 23 10 1997 18 00 00 Tomato spotted wilt virus en 30 03 2009 10 35 35 Tomato yellow leaf curl geminivirus en Tomato yellow leaf curl virus en 05 03 2009 07 21 21 Tomatoes en 05 11 1998 02 09 00 44 toi1p gt p Figure 27 Search result with search option Starts with e Ends with With this option you will retrieve the concepts labelled by terms in the languages you selected that end with the word typed in 6 2
3. 5 You will receive an email confirming that your request was sent to the VB 2 0 Administrators i e the people performing the role of Administrator for the concept scheme s you are interested in 6 You may start using VB once the Administrator approves your registration and after you receive a second email with the Subject title Activation of your account on VocBench containing your registration details 2 2 Login Once you have created an account you may access VB by entering your username and password in the User login area on the VB entry page Figure 2 After clicking on Sign in a window pops up Select the editorial role User group you wish to play during the current session and the Ontology you want to work with Figure 8 Select Preferences User group Ontology e Administrator Publisher faotopics Validator Term editors Ontology editors can manage concepts Agrovoc Skos Version and relationships They include more experienced terminologists and thesaurus editors VB 2 0 User Manual Page 16 of 101 Figure 8 Login Select preferences Note If necessary you may add a new existing ontology by clicking on the sign Figure 8 In the pop up window fill in the project ontology name a brief description the Base URI the Semantic Turkey Server URL Figure 9 and click on Add Add project Project name Project description Project type SKOS XL Base URI Semantic Turkey Serve
4. 4 Gives access to user management such as registered users new user requests Users group management of user groups Groups ontology management Ontology Configuration of VB Note Users and Groups are available to both Publishers and Administrators Ontology and Configuration are only available to Administrators see Sec 7 Editorial workflow e About VocBench Figure 13 5 Gives access to information about Partners List of partners collaborating in the development of VB Contact us Opens a web form to contact the VB team by email Note The form takes you to the Agricultural Information Management Standards AIMS website which contains a section on VB 7 http aims fao or VB 2 0 User Manual Page 20 of 101 e RSS feed Figure 13 6 Allows you to subscribe to an RSS feed to be constantly informed about the changes made in a specific dataset i e create edit delete concept terms relationships user accounts and groups new user registrations change of rights By clicking on RSS feed you open the page where you may subscribe for the VB RSS feed simply click on Subscribe Now Administration About VocBench A RSS feed Users 4 Partners 5 6 Groups Contact us Ontology Configuration Figure 13 General settings Administration 4 About VB 5 RSS feed 6 e Preferences Figure 14 7 Allows you to manage your account information preferences regarding the user interface and th
5. Home About VocBench 4 Espa ol VERSION 2 0 Build 20131025 Nederlands VocBench Welcome to the VocBench The VocBench manages concepts and terms in AGROVOC FAO s agricultural thesaurus and supports ts evolution to an ontology Username Password You must log in or create an account to use the VocBench This is the production version of VocBench used by AGROVOC terminologists If you would like to test Vocbench Pl nene please visit our sandbox version What s new orgot your username or passwogd eu Create an account e VocBench Web Services Beta version has been released for developers of agricultura informaticn management systems o incorporate the VocBench into their applications via web services VocBench Partners A Food and Agriculture Organization of the Kasetsart Thai National Agris MIM MIMOS Berhad Universit degli Studi di United Nations Gy University Center Kuala Lumpur Roma for a world without hunger Bangkok Bangkok Thailand Malaysia Tor Vergata Thailand VocBench is partially funded by the agINFRA project Acknowledgements for the revision of AGROVOC content to Acknowledgements for the contribution of ICRISAT ae agINFRA 4 ic Ki SAT international Crops Research institute for theProf Dagobert Soergel acintra EC 7th framework program INFRA 2011 1 2 2 Sconce wthatementece Semi Arid Tropics UNIVERSITY OF MARYLAND Grant agreement no 283770 Figure 1 VB entry page U
6. for the scheme you are looking at VB 2 0 User Manual Page 94 of 101 Statistics Stats on the concepts terms languages iv Total no of concepts 32 478 Total no of terms 628 730 Total no of top concepts 25 No of languages available 26 No of terms available in each language Language Term count Arabic ar 25 628 JRA bn 0 bosanski jezik bs 0 Catala ca 0 Cesky cs 40 313 dansk da 0 Deutsch de 30 732 Figure 102 Search option Stats on concepts terms languages e Select the group Stats on the structure to view the following information about the hierarchical structure Figure 103 O O O O number of concepts under each top concept only up to first level number of concepts under each top concept counting all levels below each top concept depth of branches number of levels underneath each top concept average depth of hierarchy minimum depth of hierarchy maximum depth of hierarchy number of concepts with multiple parentage number of concepts at bottom level leaves of the graph for the scheme you are looking at VB 2 0 User Manual Page 95 of 101 Statistics 2 Stats on the structure vi No of concepts under each top only first level below top Top concept s Concept count http aims fao org aos agrovoc c 13586 15 http aims fao org aos agrovoc c 49874 28 http aims fao org aos agrovoc c 9001017 8 http aims fao org aos agrovoc c 331000 10 http aims fao
7. jamesatcaas a manishps824 a tvprabhakar a nurul adilla a bramangkoun a Jasbeer Singh a atifah a ehesse a U7Fi a Figure 19 Administration Users e Groups Chat address lavanyakms Comment v Activated SKYPE lv Ontology tT agrovoc faotopics This option is used to manage user roles the associated permissions and the associations between users and roles Figure 20 Group management Existing groups Ti Group permissions Group members Group actions Search Administrator CONCEPT CRE Publisher Import Johannsen CONCEPT DELE Validator Export caracciolo CONCEPT EDIT Ontology editors Validation yjaques CONCEPT EDIT Term editors Concepts GJohannsen CONCEPT EDIT Non logged in users Statistics lavanya TERM CREATE Unassigned to any group Users TERM EDIT Visitor Groups TERM DELETE Preferences TERM RELATIO Relationships TERM RELATIO Home TERM RELATIO Configuration TERM NOTE CR Ontology TERM NOTE ED Schemes TERM NOTE DE TERM ATTRIBU TERM ATTRIBU Group description Administrators have full access to the system Figure 20 Administration Groups e Ontology This option displays the base URI and namespace of the loaded scheme Default configuration and the vocabularies used in it Namespace management From the Imports box you may import vocabularies for use within the current concept scheme Figure 21 VB 2 0 User Manual Page 26 of 101 Ontology management Default configurat
8. Click on the icon in the bar above the relation hierarchy Figure 83 a window opens with the title Create new relationship Create new relationship Label Language Select Position None Figure 89 Create new relation In the window add the following pieces of information a Label b Select Language from the drop down list c Click on the Submit button 10 2 2 Delete a relation This action may be performed by Publishers and Administrators Note This functionality is not available for imported relations 1 Select the relation 2 Click on the icon in the bar above the relation hierarchy 3 A warning message is visualized Delete relationship You are deleting the relationship testRelation Click Delete to confirm or Cancel to close Figure 90 Delete relation VB 2 0 User Manual Page 83 of 101 4 Click Delete or Cancel VB 2 0 User Manual Page 84 of 101 11 Schemes module The Schemes module is only accessible to Administrators Recent changes Concepts Relationships Validation Load data Export Statistics The module lists Figure 91 the SKOS concept schemes managed by the VB and offers the possibility to add new schemes Scheme Management sG http www w fao org landandwater s G s Lm http w w w fao org landandwater s Lm s E http wwww fao org landandwater s_E Js Wr http w w w fao org landandwater s Wr s Wr http w w w fao org landandwater s Wr s http w
9. Concepts module Visualizing the top concepts of AGROVOC If you click on any of the concepts in the concept hierarchy the screen divides into two parts as shown in Figure 49 The entire hierarchy is shown in the left side A Concept hierarchy area while the information relevant to the selected concept i e its terms information about the terms definitions relationships etc is shown in the right side B Concept term area VB 2 0 User Manual Page 56 of 101 Administration AboutVocBench Rh RSSfeed Preferences amp J Help Sign out VERSION 1 3 DEVELOPMENT VocBench Exact word Recent changes Relationships Validation Export Statistics Concept navigation history Content language Concepts C m Show URI Show also i Gaeabionta en life on earth en organisms en e G activities en Gj entities en ig events en Add new term un G features en 2 organisms Preferred y Gaeabionta en life on earth en organisms e G groups en 10 location en English en Gaeabionta y 2 life on earth Y G measure en Espa ol es Organismos Preferred W7 ra methods en Ways of doing en mM objects en Francais fr Organisme Preferred NJ G phenomena en G processes en B FX zh Preferred W ll produce en products en G Properties en Y resources en Cesky cs organismy P
10. cs Einheit de entities en entidades es entit fr varl k tr recnonapceko ekonowiuHi ognHnyji uk 3244 zh E charakteristiky cs Merkmal de features en Caratteristiche it nitelik tr puen uk FTE zh faktory cs Faktor de factors en factores es facteur fr Fattori it fakt r tr unnHHuxu uk AIS zh Co n ten t jevy cs Ph nomen de phenomena en fen menos es ph nom ne fr fenomen tr asuwa uk WE zh lokality cs Lage de location en Luogo it S Al ko Lokasi ms konum tr micuyeshaxopxeHHa uk E E l tky cs Stoff de substances en sustancias es substance fr Sostanze it madde tr peuosuHn uk y FR zh m sto cs Standort de site en Sito it AFO ko zemin tr micue uk m en cs Ma de measure en Misura it amp ko l tr mipa uk objekty cs Gegenstand de objects en objetos es objet fr Oggetti it Objek ms nesne tr r3 e c e amp lej LE r1 e r1 a organismy cs Organismus de organisms en Organismos es Organisme fr organisma ms opranuzmel ru Saye te organizma tr opraHizmu uk 4 Py zh amp lo E E procesy cs Verfahren de processes en Procesos es Processus fr 4AA Didar hi folyamat hu Processi it pracovn postupy sk s re tr npouyecu
11. Advanced search When you click on Advanced search a detailed search form displays Figure 28 In the Search in these language s box you may select languages in which you would like to search during your current session By default it lists the languages you set in Preferences i e the languages you have editing rights in see Sec 5 2 User languages amp ontologies To add a search language click on the to remove one on the icon VB 2 0 User Manual Page 35 of 101 Advanced search Exact word Clear Index Search preferred terms only Advanced search options Repository None earch in these language s Term codes Cod ode English Spanish Status All French Arabic Concept scheme Select Chinese Russian Concept relationships Ey al a Lao Also known as Farsi Term relationships Japanese Thai Concept attribute t Term attribute Figure 28 Advanced search interface An advanced search may be performed by using the same search options described in Sec 6 Search for simple search Moreover three more search options are available 1 Case sensitive Enables a case sensitive search is enabled 2 Include notes Includes also content of editorial notes scope notes and definitions in the search 3 Search preferred terms only Restricts the search to terms marked as preferred term In the Advanced search options area t
12. Create new concept Concept already exists Create a new concept Select Preferred term Delete concept Warning message Add definition Create relation between concepts Select Relationship tab Create new relation between concepts Relationship browser Create new relation between concepts Page 5 of 101 38 38 39 39 40 41 41 42 42 43 43 44 46 50 91 92 94 55 56 57 59 60 61 61 61 62 62 63 64 65 66 67 68 69 69 VB 2 0 User Manual Figure 66 Figure 67 Figure 68 Figure 69 Figure 70 Figure 71 Figure 72 Figure 73 Figure 74 Figure 75 Figure 76 Figure 77 Figure 78 Figure 79 Figure 80 Figure 81 Figure 82 Figure 83 Figure 84 Figure 85 Figure 86 Figure 87 Figure 88 Figure 89 Figure 90 Figure 91 Figure 92 Figure 93 Figure 94 Figure 95 Figure 96 Figure 97 Figure 98 Figure 99 Concept browser Search related concept Create new relation between concepts Information added Create new relation between concepts Completed Add Edit Delete term Add new term Edit term Delete term Information about a Term Tab History Information about a term Tab Relationship Information about a term Tab Attribute Information about a Term Tab Attribute Relationships module Select the required type of property Example of object properties for AGROVOC Example of Datatype properties for AGROVOC Example of Annotation properties for AGROVOC Example of Ontology proper
13. Edit term Term Cocos nucifera Language English Preferred term Figure 71 Edit term To delete a term 1 Click on the icon next to the term 2 Awindow opens showing a warning message Figure 72 3 Click on Delete if you are sure to delete the term or click Cancel Term deletion You are deleting the term French new concept Tr Confirm with the Delete button or use the Cancel button Canoe Figure 72 Delete term 9 2 3 Information about a term When clicking on a term a new window opens presenting three tabs containing the information associated to it e History Information shown in this tab Figure 73 is automatically collected by VB For each term you can see the following pieces of information VB 2 0 User Manual Page 74 of 101 Creation date Last update Status Moreover a table shows the sequence of changes applied to the term Information for coconut palm en Non preferred term History 0 Relationship 1 Attribute 1 Notation 1 Creation date 1981 01 26 07 30 00 Last update Status Published Change Old value Action User Date Figure 73 Information about a Term Tab History e Relationship In this tab Figure 74 you can visualize the term to term relations for the selected term Information for coconut palm en Non preferred term Relationship 1 Attribute 1 Notation 1 Create new relationship agrontology hasSci
14. all languages to which it is associated The entire representation of a concept often includes many terms Figure 47 Both concepts and terms participate in relationships with other concepts and terms VB 2 0 User Manual Page 54 of 101 Aquatic plants en Plante aquatique fr Piante acquatiche it Show inferred a LEN Definition 0 Notes 12 Aftribute O N Add new term Francais fr e ls Plante aquatique Preferred W Aquatic plants Preferred W English en 2 hydrophytes W 2 Water plants W Plantas acu ticas Preferred W Espa ol es vegetaci n acu tica W Flora acu tica W Arabic ar slo ls Preferred W kE Preferred W Boro W FR zh Figure 47 Representation of a concept 9 1 1 User interface The Concepts module displays the top concepts of the concept scheme you selected when you logged in In Figure 48 the top concepts are those of AGROVOC in English VB 2 0 User Manual Page 55 of 101 Recent changes Relationships Concepts rm activities en entities en E events en E factors en El ol fo E Ie lo fol fol lo lo lo lol fo lo features en E groups en E location en EE measure en methods en E objects en E organisms en E phenomena en E processes en E products en El properties en E resources en amp o lee site en E Figure 48
15. ca cs Bl da de el A en j es Flies fa ei fi ZZ a Page 44 of 101 VB 2 0 User Manual Page 45 of 101 7 Editorial workflow VB is a web based multilingual editing tool which implements a formalized workflow to allow for contributions by distributed editors The workflow supported by VB is based on two notions the fact that ontology elements have statuses and that users have editing roles Users may have more than one role assigned but they can play only one role at a time 7 1 Status of terms and concepts When a user creates or edits a term or concept the system assigns it a status of approval in the workflow Possible statuses are Proposed A user has proposed a new concept term The term concept is drafted and has not yet been approved Revised A user has revised an already existing term concept The revision has not yet been approved Validated A proposed revised term concept has been approved by a Validator Only after it has been reviewed by a Publisher will it get published Published A validated term concept has been approved and confirmed by a Publisher Only published terms and concepts are included in the public version of the schema Proposed Deprecated A user proposes to remove a term concept This needs to be approved by a Validator or Publisher Deprecated A proposed deprecation of a term concept has been approved by a Validator or Publisher The term concept
16. dropdown box i e object datatype annotation ontology properties If present the hierarchy of relations is shown VB 2 0 User Manual Page 79 of 101 When clicking on a relation in the hierarchy a right panel opens same behavior as module Concepts see Figure 82 The hierarchy list is shown on the left side while the information relevant to the selected relation is shown on the right side R skos topConceptOf Relationships Object properties v 2 showuRI R skos hasTopConcept Label 1 Definition 0 Property 0 Inverse Property 1 Domains 2 amp Ranges 2 R skos inScheme IRI R skosxtprefLabel English is top concept in scheme R skos semanticRelation amp R skosxtlabelRelation R skosxtaltLabel R skos member IRI skos memberList R skosxthiddenLabel R owlbottomObjectProperty Figure 82 Relationships user interface 10 1 1 Relation hierarchy list Starting from the left there are a number of buttons with the following functionalities Relationships Datatype properties y Figure 83 Relationships buttons e Reload relations Refreshes the screen and reloads the selected relations or the entire hierarchy list if no relation is selected e Add new relationship To add a new relation to the hierarchy list Next to these buttons there is the check box Show URI to show the URI of the selected relation VB 2 0 User Manual Page 80 of 101 10 1 2 Relation a
17. function af en El IR Is practice for en R ls post production practice for ten IR ls prevented by en i IR ls propagation process af en IR ls property af Cen IR ls theme af en IR Performs en IR Prevents en R Produces en R Product of en IRI Essive relations en IR Has hast or ls vector for en Expand al Collapse all S ubrit Lancel Figure 65 Relationship browser Create new relation between concepts VB 2 0 User Manual Page 70 of 101 Concept browser Oryza glaberrima Search View concept tree Search results Concept Last update date r Malignant catarrhal fever virus en 05 11 1998 02 09 00 ra Mycorrhizae en 13 04 2007 19 33 18 ra Endomwycorrhizae en 01 11 2009 17 00 00 ra vam fungi en Vesicular arbuscular mycorrhizae en 11 11 1997 17 00 00 Oryza fatua en Oryza rufipogon en 05 11 1998 02 09 00 Oryza indica en Oryza japonica fen Oryza sativa en 03 06 2009 06 09 45 Oryza longistaminata en 15 05 2009 12 33 27 Oryza perennis en 05 06 2009 05 44 04 Oryza punctata en 18 05 2008 12 34 54 44 stblb Submit Cancel Figure 66 Concept browser Search related concept Create a new relationship to another concept Relationship ls produced by eni Browse Related concept Oryza glaberrima en Browse Create Cancel Figure 67 Create new relation between concepts Information added VB 2 0 User Manual Page 71 of 101 v R
18. org aos agrovoc c 7778 6 http aims fao org aos agrovoc c 330829 5 http aims fao org aos agrovoc c 6211 17 http aims fao org aos agrovoc c 330705 57 http aims fao org aos agrovoc c 330704 27 http aims fao org aos agrovoc c_330998 39 http aims fao org aos agrovoc c 330988 21 http aims fao org aos agrovoc c_4788 36 http aims fao org aos agrovoc c_49904 32 Figure 103 Search option Stats on the structure e Select the group Stats on relations and properties Figure 104 to view the following information o number of concept to concept relations o number of term to term relations o number of attributes of concepts o number of attributes of terms for the scheme you are looking at Statistics e Stats on relations and properties vi No of C C relations 164 http aims fao org aos agrontology hasPropagationMaterial 5 http aims fao_org aos agrontology isBeneficialF or 49 http aims fao org aos agrontology surroundedBy 22 http aims fao org aos agrontology hasCropingSystem 0 http aims fao org aos agrontology has Theme 172 http aims fao org aos agrontologyzspatiallyIncludes 543 http aims fao org aos agrontology hasPhysiologicalF unction 8 http aims fao org aos agrontology hasGenus 3 http aims fao org aos agrontology includesSubprocess 4 http aims fao org aos agrontology isAfflictedBy 3 http aims fao org aos agrontology follows 49 http aims fao org aos agrontology isMeansF or 70 http aims fao org aos a
19. term area B Figure 52 is organized in tabs Each tab provides access to a different piece of information about the selected concept VB 2 0 User Manual Page 60 of 101 For example Figure 52 shows the tab Terms for the concept genetically modified organisms content language English ra genetically modified organisms en aa a ada ate hi C Show inferred and explicit O Definition 1 Mote 1 Attribute 0 Notation 0 Relationship 1 History 6 Image 0 Hierarchy Add new term Ai genetically modified organisms Preferred W English en Z GMoW e Genetically engineered organisms W gt refer a ada sta Preferred W o gt aati adstat sia W i deprecated Bil Sepr Show more amp FAO 2013 Figure 52 Concept term area Information tabs The following tabs are available e Terms Shows all terms associated to the selected concept in the selected languages Note To see all available terms in all languages make sure the option Show only terms of selected languages under Preferences see Sec 5 2 User languages amp ontologies is unchecked e Definition Shows the definitions available for the selected concept e Note Shows available editorial and scope notes Figure 53 VB 2 0 User Manual Page 61 of 101 Lal genetically modified orqanisms en aa ufzafda si hi Show inferred and explicit Definition 1 Coe AE Attribute 0 Add new notes Source Glos
20. to interact more 14 http openuplabs tso co uk demos sparqleditor VB 2 0 User Manual Page 100 of 101 deeply with the underlying data For instance by hitting CTRL SPACEBAR at the top of a query a list of suggestions will come up through a contextual menu If you select PREFIX normally in Flint you would have to add manually a prefix to the query In VB instead by hitting CTRL SPACEBAR again the list of actual prefixes declared in the current project will be prompted or a generic all prefixes option will immediately copy in the query a multiple PREFIX declaration containing all the prefixes declared in the project
21. to its top term Figure 57 a ACETOBACTER de Acetobacter en Acetobacter es Ac tobacter fr Acetobacter it Show inferred and explicit Terms 20 Definition 0 Note 0 Attribute 0 Notation 0 Relationships 2 History 0 Image 0 Gi Organismus de organisms en Organismos es Organisme fr rm MIKROORGANISMUS de microorganisms en Microorganismos es Micro organisme fr Microrganismi rA BACTERIA de Bacteria en Bacteria es Bacteria fr Bacteria it Figure 57 Concept term area Hierarchy VB 2 0 User Manual Page 63 of 101 In the following we highlight some crucial operations that can be performed on concepts 9 1 2 Add a new concept This action may be performed by all roles To add a new concept take the following steps 1 Choose where in the hierarchy to add the new concept 2 Click on the icon in the bar above the concept hierarchy Figure 50 a window opens with the title Create a new concept 3 In the window add the following pieces of information Figure 58 a Term for the concept b Select Language from the drop down list c Click on the Create button Create a new concept Term Language English Francais Italiano Nederlands Figure 58 Create a new concept Add term and language 4 The system checks if the suggested term is already present in VB If the label already exists you receive the message Concept already exists Figure 59
22. 0 11 2011 21 50 24 US cocona en Solanum hyporhodium en 30 08 2013 01 03 12 Le Solanum khasianum en 20 11 2011 21 47 05 ry Pepino en Solanum muricatum en 20 11 2011 21 36 43 r Solanum chacoense en 20 11 2011 21 50 24 Figure 25 Search result with search option Exact word e Exact match With this option you will retrieve the concepts labelled by terms in the languages you selected matching the exact term typed in Example A search for Solanum will in this case only return one result i e the exact term Solanum Figure 26 VB 2 0 User Manual Page 33 of 101 VERSION 2 0 Build 20131025 VocBench eec maten Je sme nt changes Concepts Relationships Schemes Validation Load data Export Statistics Concept navigation history Content language Search results Concept Last update date 1 ar Solanum cs SOLANUM de Solanum en Solanum es cic o fa Mejor ua fa as Ys fa Solanum fr AAAA hi Solanum hu Solanum it FA ja PEAIS ko Solanum lo Solanum pl Solanum pt Solanum ru 20 11 2011 21 24 22 Solanum sk Solanum th Solanum tr uk amp zh Figure 26 Search result with search option Exact match e Contains With this option you will retrieve the concepts labelled by terms in the languages you selected that contain the word or string typed in Example A search for palm returns also the terms Acer palmatum oil palms ascorbyl palmitate
23. 788 http aims fao org aos agrovoc xl cs 1299485662109 metody cs http aims fao org aos agrovoc c 4788 http aims fao org aos agrovoc xl de 1299485662139 Methode de http aims fao org aos agrovoc c 4788 http aims fao org aos agrovoc x en 1299485662168 methods en http aims fao org aos agrovoc c 4788 http aims fao org aos agrovoc xl es 1299485662199 M todos es http aims fao org aos agrovoc c 4788 http aims fao org aos agrovoc xl fa 1299485662239 A535 fa http aims fao org aos agrovoc c 4788 http aims fao org aos agrovoc xl fr 1299485662278 M thode fr http aims fao org aos agrovoc c 4788 http aims fao org aos agrovoc x hi 1299485662314 faerat Tita hi http aims fao org aos agrovoc c 4788 http aims fao org aos agrovoc xl hu 1299485662353 m dszer hu http aims fao org aos agrovoc c 4788 http aims fao org aos agrovoc xl it 1299485662400 Metodi it FAO 2014 Figure 107 SPARQL querying VB The checkbox at the bottom left of the query area Include inferred statements Figure 107 sets a parameter in the query so that it includes or ignores triples inferred by reasoner from the search space The two buttons at the bottom right Clear and Submit Figure 107 allow respectively for cleaning the query area and for submitting the query The UI engine behind this interface is based on Flint an open source web editor for SPARQL offering syntax completion and highlighting In VB Flint has been customized
24. Figure 33 Figure 34 Figure 35 Figure 36 Figure 37 Figure 38 Figure 39 Figure 40 Figure 41 Figure 42 Figure 43 Figure 44 Figure 45 Figure 46 Figure 47 Figure 48 Figure 49 Figure 50 Figure 51 Figure 52 Figure 53 Figure 54 Figure 55 Figure 56 Figure 57 Figure 58 Figure 59 Figure 60 Figure 61 Figure 62 Figure 63 Figure 64 Figure 65 Advanced search Search preferred terms only by Relation AND Word Results of Advanced Search Search by Concept AND Relation Advanced search Search for term codes Select repository Advanced search Search for term code Advanced search Search for status Proposed deprecated Advanced search Search for concept attribute Advanced search Search for Fishery related term Advanced Search Search for term attribute Advanced Search Search for Common name for plants Search area Concept navigation history Concept navigation history Content language Legend RSS feed VB module Recent Changes Recent changes filter Representation of a concept Concepts module Visualizing the top concepts of AGROVOC Concept hierarchy area A and Concept term area B Buttons on concept hierarchy area Graph visualization of a concept Concept term area Information tabs Concept term area Note Concept term area Attribute Concept term area Relationship Concept term area History Concept term area Hierarchy Create a new concept Add term and language
25. L VB 2 0 User Manual Page 2 of 101 Table of Contents EXECUTIVE SUMMARY Ada 1 TABLE OF CONTENTS aa A A AA 2 LUST OF FIGURES cun duced caucengus Caeeutuc urs vaeucduasdoucuuweneuctaeeunususepawedbandeucevevaeuecnteuuweuavadus Eaa 4 LEGEND 8 np ellegpee c doi 9 PM REGISTRATION amp LOGIN od 11 ZERE STE RE or o ES E T TT 12 22 OGN dd 15 3 USER INTERFACE Joc sue uuu audeo du uek cua A AA 17 SINISTRE 18 3d General sett a ius ou eo d vaste o oa ou eu Pete dae a uae RU Rede de lu mud eu UM AAA Leu M MMC I UD OU DM Ue 16 LANI IO vo RT J 21 3 1 3 Access to CONTENTS IO QUID Fi iode eeu ote sae A d o and aseo eau dan doe deu crate AS veu ea D Vea ad 21 3 1 4 Concept navigation history amp Content language c ooocccnncnncnccncnncnnnnonnonocnnnacnnnnonnnnocnonornnnncnnnnconononnonocnnnnccnononos 23 2 ADMINISTRALTION eransi tinna Eu MERE MP CENE BraRu EE E Ca cues EORR e a V AF cU is 24 S RRE PER EN CE 5 RP cate 27 5 EDETALS OF YOUR USER ACCOUNT a ii 28 5 2 USER LANGUAGES SEONTOLOCIES daa 29 6 SEARCH nia M 31 b ESIMPLESEARC A catalana totali aia labora Des 31 0 2 ADVANCED SEARCH A A A AAA AA AA 34 6 2 1 Search for relationships between Conc pte cutanee E AE E E AA 35 6 2 2 Sedrch by both relation AND concept ioo n
26. Note These settings will be saved also for your next sessions 3 Filter by status By default all term statuses are unselected To modify the selection simply check the appropriate check boxes Note These settings will be saved also for your next sessions 4 Filter by date You may narrow the time span down by using the options in the Filter by date box VB 2 0 User Manual Page 89 of 101 5 Page size Figure 96 bottom left corner It allows to enter the number of entries you would like to see displayed per page To apply the filter click on Submit 12 2 Validate a change The following steps are to be followed in the validation process 1 To validate the changes one by one navigate to the Validate column 10th column of table and select from the dropdown box either Accept or Reject Alternatively check at the bottom of the Validation module the checkbox Accept all or Reject all In the Note field last column of table the Validator may enter a comment for example explaining why a change was rejected 2 After accepting or rejecting the issues click on Validate in the bottom right corner 3 After validation by a Validator the element becomes red if it was a revision and green if it was newly created The status of the element is changed to Validated After validation by a Publisher the element becomes blue and its status Published 4 The Modifier will be informed by email that his her changes were accepted or r
27. Relationship Search in these languac Include notes 2 Search preferred terms only 2 English Repository None Code Term codes Classification scheme Select i Status All El i Concept attribute Term attribute Figure 31 Advanced search Search preferred terms only by Relation AND Word VERSION 1 3 DEVELOPMENT Voc Bench Exact word E Recent changes Concepts Relationships Validation Export Statistics Concept navigation history Content language Search results Concept Relationship Concept African horse sickness virus en Causes en African horse sickness en African swine fever virus en Causes en African swine fever en Aujeszky virus en Pseudorabies virus en Causes en Aujeszky s disease en Pseudorabies en Banana bunchy top virus en Causes en Bunchy top disease en Bluetongue virus en Causes en Bluetongue en Borna disease virus en i Causes en Borna disease en Bovine leukaemia virus en m 1 Causes en Bovine leukosis en Bovine leukosis virus en Bovine oncovirus en en en Carre s disease en Carre s disease virus en Distemper virus en Causes en Distemper en Canine distemper en id 12 gt Figure 32 Results of Advanced Search Search by Concept AND Relation Note You may search for relationships between terms in the same ways as described for concepts using the Browse button of the Term
28. VocBench v2 0 User Manual Last update March 2014 Based on VocBench v2 0 Prepared by Caterina Caracciolo FAO Sarah Dister FAO Gudrun Johannsen FAO Lavanya Neelam Sachit Rajbhandari FAO Armando Stellato Food and Agriculture Organization of the United Nations India University of Rome Tor Vergata Italy Please contact us at aims fao org VB 2 0 User Manual Page 1 of 101 Executive summary This manual provides instructions on how to use VocBench version 2 0 VB 2 0 a web based vocabulary management tool providing full multilingual support and enabling a formalized workflow It covers editorial operations typically performed by VB Editors Validators and Publishers It also covers functionalities for Administrators but only limited to the management of projects i e not including global system configuration administration The manual first explains how to create a user account Sec 2 Registration amp login specify your user and interface settings Sec 4 Administration and 5 Preferences and interpret the user interface Sec 3 User interface This is followed by sections on how to search VB Sec 6 Search and on the various roles a user may play in the workflow Sec 7 Editorial workflow Subsequently each module is covered in a separate section in the following order Recent changes Concepts Relationships Schemes Validation Load data Export module Statistics and SPARQ
29. and a short link to the existing concept is provided In that case enter a new term and click on Check availability then follow steps 4 to 7 Note Take Care The fact that you receive a message informing you that the term already exists does not stop you to create the term anyway VB 2 0 User Manual Page 64 of 101 Create a new concept Term Soil horizons Language English se Concept already exists Check avadab ty Concept Last update date i Soil horizons en Horizon du sol fr Orizzonti del suolo it 02 09 2013 18 34 54 Figure 59 Create new concept Concept already exists If the label does not exist a new window opens Here you choose Figure 60 a The position in the hierarchy where the concept should be added The following possibilities are available i Child of the selected concept ii Same level as the selected concept iii Top level concept b If the new term will be a preferred term by checking the box or not Note Currently the box Preferred is checked by default Figure 60 when a concept is new but if you add more labels it is unchecked VB 2 0 User Manual Page 65 of 101 Create a new concept Term Language Position A ivi Preferred term 3 Show advanced options 2 Figure 60 Create a new concept Select Preferred term 5 Then click Add or Add and repeat if you want to create another term or Cancel to abandon 6 After clicking Add the system takes y
30. anguages in which you would like to edit concepts see Sec 5 2 User languages amp ontologies VB 2 0 User Manual Page 24 of 101 4 Administration Administration is available from the top menu bar Figure 18 After clicking on it you have four options e Users e Groups e Ontology e Configuration Sign out Ontology Configuration Figure 18 Top menu bar Administration Ontology and Configuration are only available to Administrators Users and Groups are available to both Publishers and Administrators e Users This option shows the users using the same VB installation as you For each user user details user group s language s and ontolog ies are indicated Figure 19 VB 2 0 User Manual Page 25 of 101 User Management Users Y Active Y Inactive M New User details User group s Administrator a P Publisher Publisher a A Username lavanya Validator Validator a Ontology editors Ontoeditor a Password Confirm password Term editors Termeditor a Administrator poem or M First name lavanya Last name Kiran caracciolo a E SESS TR yjaques a Email lavanyakirann gmail coi Affiliation ICRISAT Language s lavanya a yingsean a Address 212 KSI ICRISAT Postal code English zuzana_horvathova agroinstitut a E cklee75 a supiah a leza a par URL Registration date 29 112013 beikzadeh a saniah a Work phone Mobile phone 91 9177609798 Country India v Bevro
31. are those who have the total control of the concept schema and are responsible for publishing the validated entities Publishers have all the rights of Term Editors Ontology Editors and Validators The following describes publishers roles and privileges Publishers have access to the following modules e Recent changes e Concepts e Relationships e Validation VB 2 0 User Manual Page 49 of 101 e Export e Statistics In the Concepts module Publishers may perform all actions allowed to Term Editors Ontology Editors and Validators plus the following ones e Move link and unlink concepts In the Validation module they may perform the same actions as Validators e Permission on terms and concepts e Validate changes applied by Editors and confirm changes applied by Validators In the Relationships module they may create new relations between terms and concepts They ultimately approve a validated entry by a Validator and change its status to Published e They can still reject validated entries and thus remove them again from the model in case of new proposals or reset them to their previous status in the case of Proposed Deprecated Finally Publishers have access to the link Administration in the menu area from where the Users and Groups menus are available 7 2 5 Administrators Administrators have access to all VB modules and have overall rights VB 2 0 User Manual Page 50 of 101 8 Recent
32. ator This module is used to import RDF data by providing the base URI and RDF file see Sec Load data module e Export All roles To export a concept schema in SKOS XL format or to export a concept in SKOS XL format with the option to include its children see Sec 14 Export module VB 2 0 User Manual Page 23 of 101 e Statistics Administrator Publisher Validator amp Ontology Editor To search for statistics referring to the content contained by VB from the workflow to concepts terms relationships etc see Sec 15 Statistics e SPARQL Administrator To query update all content through the SPARQL query update language for RDF see Sec 16 SPARQL module 3 1 4 Concept navigation history amp Content language Two more buttons Concept navigation history and Content language are available in the bottom menu bar C of the menu area see Figure 15 and Figure 17 Concept navigation history Content language Figure 17 Menu area C Concept navigation history amp content language e Concept navigation history All roles The navigation history shows the list of concepts navigated during your current session see Sec 6 3 Concept navigation history e Content language All roles To select the languages in which you want to search and visualize concepts Note The languages you select here are only related to searching and visualizing and only for the current session In Preferences you may set the l
33. box see Sec 9 Concepts module The information shown in this tab is automatically collected by VB For each concept term the creation date last update and status is displayed Recent changes Concept Term Relationship Users Change Ej Photosyst me fr Fotosistemi it Fotosistemas es T fotosistem tr PHOTOSYSTEM de Photosystems en C CHLOROPLAST de Cloroplasti it chloroplasts en TJ kloroplast tr Chioropiaste fr Cloroplasto es IG Amioplasto es AMYLOPLAST de Amyloplast en T amiopiast tr Amyicplaste fr Amiloplasto t lO PLASTID de Plastics 11 Plastidios es Plastids en TJ plastit tr Paste fr WG Cell nucieus en Nucieo della calula t N cleo es Noyau cellulare fr ZELLKERN de nucleus en NUCLEUS T h cre ekirde i tr de Nucleo 1 LG Cell nucleus en Nucleo della celula t N cleo es Noyau cellulare fr ZELLKERN de nucleus en NUCLEUS T nukleus tr de Nucleo t O Cell nucleus en Nueiea della celula N cleo es Noyau cellulare fr ZELLKERN de nucleus en NUCLEUS iT cekirdek tr de Nucko 1 O Miocondris es CHONDRIOSOM de Condrioma es Condriosomi 4 Condriosomas es Chondriome fr j l S Lj kondriyozom tr Chondriosomes fen Mitochondria en Mitacondri 11 Figure 45 VB module Recent Changes 8 1 Apply filter options Old value Fotosistemier tr
34. cent changes that have taken place in VB and need to be validated Recent changes Concepts Relationships mies Validation Load data Export Statistics When entering the Validation module Figure 95 you will see in ascending chronological order the list of all actions to be validated Validatio Concept Term Rela Change Old value vey actividades es LT activities en 7 activities en activit fr activities en WG Insecta en UE ndlelugu te Insecta fr Insects en Insecte fr INSEKT de Insectos es Insecta es INSECTA de e new term en I new term en e new term en WE new term en T Insects en R Has translation en D 29 v Figure 95 Validation module Action term edit term create concept delete concept delete term relationshi Owner Modifier Creation dat Modified dat Administrator Administrator 24 09 2008 Johannsen Johannsen Johannsen lavanya Johannsen Johannsen Johannsen lavanya 18 00 00 05 09 2011 09 36 57 05 09 2011 10 29 16 05 09 2011 10 29 16 05 09 2011 12 46 16 11 08 2011 10 25 12 05 09 2011 09 36 57 05 09 2011 10 30 22 05 09 2011 10 38 12 05 09 2011 12 46 16 Status Validate Revised Accept Reject Proposed Accept Reject Proposed depre Accept Reject Proposed depre Accept Reject Pro
35. changes module This module gives an overview of all changes applied to a given scheme since its loading in VB By default the list of changes is presented in reverse chronological order i e latest first Error Reference source not found A change is split in 6 aspects columns of which each provides a different type of information about the change 1 Concept Term Relationship Users Shows the concept when the change belonged to the concept e g the creation of new concept a new term a new concept to concept relationship Shows the term when you add any term term relationship Shows the relationship when you make any changes in the relations in the Relationship module 2 Change shows the actual new value e g the new term 3 Old value shows the value before the change took place 4 Action indicates which action was taken e g term create 5 User shows the name of the user who performed the action 6 Date indicates the date and time of the action Other ways to be informed about changes e Subscribe to the RSS feed available in the top menu bar Figure 44 Administration AboutVocBench Ly Preferences Help 0 Sign out Exact word Advanced search concept navigation history Content language Figure 44 RSS feed VB 2 0 User Manual Page 51 of 101 e Select a concept in the Concepts module and open for concepts the History tab in the concept box and for terms the History tab in the term
36. cs dansk da Deutsch de AArjvikG el English en Espa ol es Persian fa suomi suomen kieli fi vosa Vakaviti fj Fran ais fr O Nc COND0o AANA Om Figure 106 Option on Stats on workflow VB 2 0 User Manual Page 98 of 101 16 SPARQL module The SPARQL query module contains e A menu box for selecting the SPARQL operation QUERY or UPDATE and language version SPARQL 1 0 or 1 113 e Atextarea where to write the SPARQL query e Anarea showing the results in a table 13 since VB can be used with different RDF middlewares restricting the language version to SPARQL 1 0 can be useful for those connected middlewares which do not support SPARQL 1 1 VB 2 0 User Manual Page 99 of 101 VERSION 2 0 1 SNAP SHOT Build 20140221 DEVELOPMENT VocBench SpE Recent changes Concepts Properties Schemes Validation Load data allis SPAROL Concept navigation history Content language SPARQL query Query language SPARQL 1 0 PREFIX lt http aims fao org aos agrovoc gt 2 PREFIX skos http www w3 0rg 2004 02 skos core PREFIX skosxl http www w3 org 2008 05 skos xl SELECT WHERE c a skos Concept c skosxl prefLabel xl xl skosxl literalForm 1f LIMIT 10 Line 6 Position 1 Query is valid Sa statements e Submit c xl If http aims fao org aos agrovoc c 4788 http aims fao org aos agrovoc xl ar 1299485662065 lt i ar http aims fao org aos agrovoc c 4
37. csecccuuecsceueecccuueccsseecssusecscuuecessusecssaeesens 66 I2 OPERATIONS ON TERS Sons a daa aaa dal dada das 71 DDT AO Gite W TEM O e ce eee a A estes e A AO a 71 ODD POOF deleted Tet scs MR MM EU ee ee ee 7 2 92 3 Information dDOUEG Celi ecd caso notae tci aeterne AAA qu Ie ts a va aded adeo Duo Reden teles Sa a Pe reta 73 9 2 4 Edit Information about ATAN A A AAA A AA cu e ule OR i 75 TO RELATIONSHIPS MODULE ica a a A v ats 76 TOL USERINTEREACE E E E E E A AEE E T EE T EE EE E T 78 TOL L Relation Mero o T 79 TOT REO UOC ds AE A lo te o te lo de EOE A A A E E E A A PENET SO 10 2 OPERATIONS ON RELATION Sa eo epe E RE ci abuso A A a Pate co n aa ete Gea aes 81 QI10 2 LAO dnewtelatiQh oo ee shee e e RE es RE oO l 10 2 Derete QTelatiol iuo OR Re a Ste Re Soe eT eee rea 82 t1 SCHEMES MODULE iii A a A 84 TLF ADD ANEW CONCEPT SCHEME seccatid 85 12 VALIDATION MODULE 0 loas 86 AED TNT EMD ATION di teats 87 IIA DATE A CHANGE caer tete Coe sedente cin delis had etie vp tb Sorte emai oats ra i ACE ite Petr cuu dede nde tam tatiana ites 89 13 LOAD DATA MOD ULE o a i 90 TA EXPORT MODULE aiii di dat 91 TS TATS MES A td diaria adan 93 16 SPARQL MODULE idictiise or tux deua nna dua alu de nux unus E eia eaux COE kUNU ax de eau aa Cua ra BEEN dud 98 VB 2 0 User Manual List of Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 Figure 7 Figure 8 Figure 9 Figure 10 Figure 11 Figure 12 Figure 13 F
38. d and explicit By default VB shows only explicit information Checking this option reasoned and inferred relationships are constructed based on OWL reasoning using information already explicitly provided by editors and publishers The inferred information will be shown in light grey and will not be editable to make changes one should change the explicit information from which they are derived 5 2 User languages amp ontologies User Language This box lists the languages in which you are allowed to edit the data you have access to Figure 23 In case you want to remove any language s select the appropriate language s and click on the button If you want to request editing rights to a new language for editing concepts terms click on the icon select from the dropdown list the language and click on Add After this step the selected language will be added to Pending language request box The VB Administrator will receive an email about your language request After approval you will be notified by email VB 2 0 User Manual Page 30 of 101 Note These language settings refer to editing rights To define the languages in which you would like search and visualize concepts terms use the orange Content language button available in the bottom right corner of the menu area Note The Show only terms of selected languages check box in the left panel refers only to the terms e Pending language request This box li
39. dministrators To edit any of the pieces of information attached to a concept 1 Select the concept in the concept hierarchy 2 Click on the appropriate tab In the following the most relevant actions on concepts are singled out and explained in detail e Add a definition to a concept To provide a definition for a concept follow these steps 1 Click on Add definition 2 A window opens Figure 62 in which the following pieces of information should be added o Definition VB 2 0 User Manual Page 67 of 101 o Language select language from drop down list o Source for the definition Possible sources are e g Wikipedia o URLfor the source 3 Click Create or Cancel Add definition Definition Language Select ES Source A i URL FAOTERM NAL WIKIPEDIA MeSH Other Book Journal Article AGROVOC Wordnet Figure 62 Add definition e Edita definition of a concept It is possible to edit the entire definition or the source 1 Click on the Edit icon of the item you want to edit 2 Revise definition and submit your changes e Delete a definition of a concept 1 Click on the Delete icon next to the item you wish to delete 2 Delete and confirm e Add a relationship to a concept To create a relation between two concepts follow these steps VB 2 0 User Manual Page 68 of 101 1 2 G Rice fen Select the first concept by browsing or searching Click on the Relat
40. ds en E LG objects en r3 organisms en phenomena en E O processes en E C products en 0 properties en E resources en Figure 100 Export module Top concepts of selected scheme To start the export click Export in the bottom right corner Figure 99 12 Limited to SKOS XL Will be extended to cover traditional SKOS core syntax for labels in future versions VB 2 0 User Manual Page 93 of 101 15 Statistics The Statistics module is accessible to Ontology Editors Validators Publishers and Administrators It gives you the ability to search for specific facts and numbers of a scheme and its editorial status Click on the Statistics dropdown box to select the group of statistical data you are interested in Figure 101 Recent changes Concepts Relationships Validation Export statistics Statistics Select statistical type stats on the concepts terms languages Stats on the structure stats on relations and properties stats on Agrovoc specific relations and properties stats on workflow Figure 101 Statistics module Select the required group e Select the group Stats on concepts terms languages Figure 102 to be informed about o total number of concepts o total number of terms preferred and non preferred o total number of top concepts o total number of languages in which the scheme is available o total number of available terms by language
41. e languages in which you want to edit data see Sec 5 Preferences Note You may also change your password in this section e Help Figure 14 8 Links to this document the VB v 2 0 user manual published on the AIMS and VB project websites e Sign out Figure 14 9 To sign out of VocBench Preferences Help Q Sign out La Figure 14 General settings Preferences 7 Help 8 Sign out 9 VB 2 0 User Manual Page 21 of 101 3 1 2 Search The search bar is always available to all users e Simple search Figure 15 Type in the term or phrase you are looking for choosing one of the options from the dropdown list and click GO For a detailed description see Sec 6 1 Simple search Exact word Exact match Contains otatistics Concept navigation history Content language Starts with Ends with Figure 15 Menu area B Simple search e Advanced search Opens an advanced search interface that allows you to use more specific search criteria For a detailed description see Sec 6 2 Advanced search 3 1 3 Access to content Module bar The module bar is shown in the bottom menu bar marked C in Figure 11 Each module is briefly described indicating the user group which is allowed to access it Note Another simple way to find out if a module is accessible to your user role is to check the colors of the module names in the module bar white names are accessible grey ones are not Recent change
42. e selected concept to a new child concept VB 2 0 User Manual Page 58 of 101 Unlink concept To unlink the selected concept from the hierarchy e Add concept to scheme H VB supports the management of multiple schemes inside the same project This functionality allows you to make the concept also belong to another scheme within the same project e Remove concept from scheme The opposite of the above allows you to detach a concept from a given scheme e View graph Opens a new window or tab with a graphical representation of the selected concept and its relations with other concepts Figure 51 8 http www w3 org TR skos reference schemes 9 For now up to a limited extent Works perfectly when schemes are meant have no concept overlap There is limited support for having concepts belong to more schemes VB 2 0 User Manual Page 59 of 101 oes VocBench Version 1 3 L m VocBench Graph Visualizat C Q 2023 13 50 snchdevv1 3i arai Zoom v 4 l N a related type pan Is sub concept of gt mm imerprolific animals en Figure 51 Graph visualization of a concept Next to these buttons there are two check boxes to select what to show in the concept hierarchy Figure 50 e Show URI Shows the URI of the selected concept e Show also non preferred terms Preferred terms are displayed in bold and non preferred terms are shown next to them Concept term area B The concept
43. ejected by the Validator Note After each validation you should refresh the validation list by clicking on the refresh button at the top left of the Validation module Figure 95 and Figure 97 in order for the system to load the new statuses of the elements Validation Concept Term Refresh validation list Figure 97 Refresh validation list VB 2 0 User Manual Page 90 of 101 13 Load data module Recent changes Concepts FRelationships A Ea Load data Maeqala y Statistics The Load data module is only accessible to Administrators It is used to bulk load RDF data to the current project This data will be merged with the data currently available in VB This functionality is intended for low level operations carried out by Administrators Import Base URI RDF file No file selected Figure 98 Load data module Provide the base URI of your data in the Base URI field and upload the RDF file by using the Browse button Upon clicking the Import button in the bottom right corner your data will be uploaded in VB Note The data you loaded will be visible only if it is compliant with that in the project For example the base uri of the loaded data should be the same as the one of the project into which it is being loaded VB 2 0 User Manual Page 91 of 101 14 Export module The Export module is available to all users It is used to export either an entire concept scheme or a single concept from a concept sche
44. ent of SKOS XL thesauri Some new functionalities for the end users are e Multi scheme management to develop several skos ConceptSchemes for the same dataset providing different views on the data e Statistics module to provide statistical information about the loaded data e Export module to export the whole or a part of the content of a project e Load data module to load bulk data serialized in some RDF serialization standard http aims fao org tools vocbench 2 http vocbench uniroma2 it http www fao org home en http art uniroma2 it http www mimos my gt http aims fao org standards agrovoc about VB 2 0 User Manual Page 10 of 101 e SPARQL module to query update content directly through the SPARQL query language for RDF e Ontology Import Management to owl import ontologies to be used as property vocabularies for the modelled thesauri e New tabs under the concept view for covering extensively the SKOS XL standard note notations VocBench has been successfully tested on the following browsers Safari Google Chrome Mozilla Firefox and Internet Explorer 6 VocBench has been tested on all the recent versions of the reported browsers and seems to work seamlessly VB 2 0 User Manual Page 11 of 101 2 Registration amp login To access VocBench you first need to register as a user Go to the User login area on the VB entry page Figure 1 and click on Create an account Figure 2
45. entificName 2 Cocos nucifera en Figure 74 Information about a term Tab Relationship e Attributes In this tab you may see the attributes assigned to the selected term In Figure 75 attributes for a term in AGROVOC are shown VB 2 0 User Manual Page 75 of 101 Information for coconut palm en Non preferred term History 0 E uU Notation 1 Add new attributes agrontology has l ermType Z Common name for plants Figure 75 Information about a term Tab Attribute e Notation In this tab one may see the AGROVOC term code given to the selected term In Figure 76 notation for a term in AGROVOC are shown Information for coconut palm en Non preferred term History 0 Relationship 1 Attribute 1 Dc ep Add new notation Notations Value skos notation zl 9965 Figure 76 Information about a Term Tab Attribute 9 2 4 Edit information about a term 1 Click on the term a window opens with the three tabs shown in Figure 69 2 Click on the tab Relationship or Attributes to add edit or delete information VB 2 0 User Manual Page 76 of 101 10 Relationships module The Relationships module is available to Publishers and Administrators It is used to add relations These relations are available in the Concepts module to create concept to concept and term to term relationships Click on the Relationships dropdown box to select the type of properties you are interested
46. etails you will need to sign out and login again to see the changes Exact word x Advanced se Signed in as Johannsen Administrator to agrovoc Administration AboutVocBench A RSS feed VERSION 2 0 Build 20131025 VocBench Recent changes Concepts Relationships Schemes Validation Load data Export Statistics Concept navigation history Content langu Details User language User ontology Login Johannsen PES New password Confirm password Portuguese Czech Lao Also known as Farsi Japanese Thai Hindi Email gudrun johannsen fao org New email Confirm email Pending language request Pending ontology request Ontology agrovoc Swedish Set your landing page Concepts anguage of the interface English en a Show URI L Show also non preferred terms Show only terms of selected languages Hide deprecated terms and concepts Show inferred and explicit Save Clear Figure 23 Personal preferences in VB VB 2 0 User Manual Page 28 of 101 5 1 Details of your user account The details of your user account are displayed in the panel on the left Figure 23 Here you may control your personal information e Login User name Note The user name cannot be changed e New password Confirm password You may change and confirm your password in this field e Email Shows your current email address e New email You may change your email in this field c
47. grontology isCompositionOf 124 Figure 104 Search option Stats on relations and properties e Select the group Stats on Agrovoc specific relations and properties Figure 105 to view the following information VB 2 0 User Manual Page 96 of 101 o number of subvocabularies of concepts chemicals Geographical Country level Fishery related terms etc o number of subvocabularies of terms taxonomic terms for bacteria plants animals common name for plants viruses animals etc Note This group is specific to the AGROVOC concept scheme Statistics Stats on Agrovoc specific relations and properties vi ja 288 Common name for viruses 53 lo 1 Sk 3 zh 3 it 3 hu 2 ko 2 fa 3 ar 1 hi 3 th 3 cs 3 de 9 pl 3 pt 2 en 6 ru 2 es 1 ja 3 Common name for plants 8 742 lo 17 Sk 632 zh 332 it 526 tr 12 ms 1 Figure 105 option Stats on Agrovoc specific relations and properties e Select the group Stats on workflow Figure 106 to view the following information o total number of users o lastuser connected o number of users by language o last modification by each user o number of exports for the scheme you are working on VB 2 0 User Manual Page 97 of 101 Statistics e Stats on workflow v User information Total number of users 56 Last user connected Administrator Count number of users assigned for every language Language User count Arabic ar TT bn bosanski jezik bs Catal ca Cesky
48. he following constraints down below to the search criteria may be applied 6 2 1 Search for relationships between concepts To search for relationships between concepts click on the Browse button Figure 28 in the Concept Relationships field open the Relationship browser select the relation you want to search for and click on Submit To perform the search click on the Search button VB 2 0 User Manual Page 36 of 101 In Figure 29 the relation Produces was selected in the Relationship browser The search result consists of all pairs of concepts being linked by that relation Figure 30 Relationship browser R ls practice for en IR Is post production practice for en R Is prevented by en R Is produced by en IR ls propagation process of en R Is property of en R Is theme of en R Performs en R Prevents en R en R Product of en a RI Essive relations en R Has host or Is vector for en R Has substitute en R Has symptom en R Has type en R Has vector or Is host for en D Reload relationship Expandall Collapse all Figure 29 Advanced search Search by relation VB 2 0 User Manual Page 37 of 101 VERSION 1 3 DEVELOPMENT VocBench Stats wth E Advanced search Last results Recent changes Concepts Relationships Validation Export Statistics Concept navigation history Content language Search results Concept Relationship Concept ul Agricultu
49. ice en Terms 33 Definition 0 Mote 07 Attribute 107 Relationships 2 History 0 Image 0 Add new relationship Relationship Concepts amp o Oryza indicateny Oryza sativa en Oryza japonicaten ls produced by end o Zii iG Oryza glaberrima eny African rice en Figure 68 Create new relation between concepts Completed 9 2 Operations on terms Terms associated to concepts are displayed in the concept term area of the Concept module Figure 49 9 2 1 Add a new term 1 To add a new term click on Add new term Figure 69 2 In the window that opens add the term select the language from the drop down list and decide if the new term is a Preferred term or not Figure 70 3 Click Submit or Cancel VB 2 0 User Manual Page 72 of 101 uni coconut palm en Cocos nucifera en Uu Definition 0 Note 0 Attribute O Relationships 12 Add new term anguage Term ocos nucifera Preferred W English en coconut palm y Cocos nucifera Preferred WJ 2 Cocotero W Figure 69 Add Edit Delete term Add new term New term o Select E a a IU MMMM THUS z Add and Repeat Cancel Figure 70 Add new term 9 2 2 Edit or delete a term To edit a term 1 Click on the edit icon next to the term Figure 69 7 2 In the window Figure 71 that opens revise the term and click Submit or Cancel VB 2 0 User Manual Page 73 of 101
50. igure 14 Figure 15 Figure 16 Figure 17 Figure 18 Figure 19 Figure 20 Figure 21 Figure 22 Figure 23 Figure 24 Figure 25 Figure 26 Figure 27 Figure 28 Figure 29 Figure 30 figures VB entry page User login User registration form Select user group Select language Select ontology Registration confirmation Login Select preferences Login Add ontology project VB user interface Concepts module menu I and content area II VB user interface Menu area General settings User name 1 User role 2 Dataset 3 General settings Administration 4 About VB 5 RSS feed 6 General settings Preferences 7 Help 8 Sign out 9 Menu area B Simple search Menu area C Access to content Module bar Menu area C Concept navigation history amp content language Top menu bar Administration Administration Users Administration Groups Administration Ontology Administration Configuration Personal preferences in VB Search options Search result with search option Exact word Search result with search option Exact match Search result with search option Starts with Advanced search interface Advanced search Search by relation Results of Advanced search Search by relation Page 4 of 101 11 11 12 13 13 14 15 16 16 18 18 19 20 20 21 21 23 24 25 25 26 26 27 31 32 33 34 35 36 37 VB 2 0 User Manual Figure 31 Figure 32
51. in Figure 77 Note Imported relations are not editable meaning that functionalities as Add Edit Delete a relationship label and Edit the information attached to a relation are not available for these relations Note All examples are taken from the AGROVOC concept scheme Relationships Object properties v i2 Obiect properties skos hasTo Datatype properties Annotation properties skos insche Ontology properties zm m skosxl prefL abel Figure 77 Relationships module Select the required type of property e Object properties Object properties relate objects to other objects For object properties one may define domain and range Admissible entities in the range of an object property are resource represented with an URI e g an skos Concept 10 For example in Figure 78 the object properties used for AGROVOC are listed 10 Steven J Miller Introduction to Ontology Concepts and Terminology 2013 In International Conference on Dublin Core and Metadata Applications DC 2013 Lisbon Portugal 2 6 September 2013 Tutorial OWL 2 Web Ontology Language Second Edition W3C Recommendation 11 December 2012 VB 2 0 User Manual Page 77 of 101 ti Relationships Object properties Y skos hasTopConcept El skos inscheme skosxlprefL abel El skos semanticRelation E skosxllabelRelation skosxl altL abel skos member skos memberList skosxl hiddenL abel m D D D D D D D D D owl bottomObjectPrope
52. ion Base URI http aims fao org aos agrovoc Default namespace http aims fao org aos agrovac Namespace management Namespace prefix Namespace http aims fao org aos agrovoc amp lenzvl httn ananw w3 nm 2008 05 skcenscv EZ Imports http aims fao org aos agrontology Figure 21 Administration Ontology e Configuration This option is used to manage the configuration of the present installation Figure 22 VocBench Configuration VERSION E 20 DISPLAYVERSION 2 2 0 Build 20131025 MODE PRO SANDBOXLINK e http 202 73 13 50 55481 vocbench WEBSERVICESINFO 2 http aims fao org tools vocbench access VOCBENCHINFO http aims fao org tools vocbench 2 CONTACTUS http aims fao org contact COPYRIGHTLINK 2 http www fao org corp copyright en DB CONNECTIONURL e jdbc mysq l localhost 3306 administrator_version207requireSSL falsesamp useUnicode truegamp characterEncoding U DB USERNAME E root Figure 22 Administration Configuration VB 2 0 User Manual Page 27 of 101 5 Preferences The Preferences button is available from the top menu bar It is used to manage the preferences associated to your user account Figure 23 In particular e Details of your user account e User language to edit data in e Pending language request e User ontology e Pending ontology request Note Your preferences will be saved and will apply to the current and future sessions If you change any preference d
53. ionship tab Figure 63 Click on Add new relationship A popup window will appear where you can specify the relation to use and select the other concept in the relation Figure 64 To select a relation click on the Browse button and the Relationship browser will open Figure 65 To view the complete list of relation types click on Expand all at the bottom of the window and select from the list the appropriate new relation To select the second concept in the relationship click on the Browse button The Concept browser will open where you can search and browse for the desired concept Figure 66 Once the concept is identified click Submit or Cancel Click the Create button to confirm the new relationship Figure 67 The new relationship is now visible in the Concept Term Area Figure 68 Terms 33 Definition 01 Mote 01 Attribute 01 Relationship 17 History 07 Image Un Add new relationship Relationship Concepts ls produced by en S Gl Oryza indica eny Oryza sativa en Oryza japonica ern Figure 63 Create relation between concepts Select Relationship tab VB 2 0 User Manual Page 69 of 101 Create a new relationship to another concept Relationship Mone Browse Related concept Mone Browse Create Lancel Figure 64 Create new relation between concepts Relationship browser R I object of activity en d IR ls pathogen of ren IR ls performed by en IR ls physiological
54. is considered as outdated VB 2 0 User Manual Page 46 of 101 Note The legend for the status of concepts and terms is always visible at the bottom of the Concepts and Relationships modules Figure 43 Legend Proposed W Validated M Published M Revised Proposed deprecated W Deprecated Figure 43 Legend 7 2 User roles Possible roles in the workflow are 1 Term Editor 2 Ontology Editor 3 Validator 4 Publisher 5 Administrator Note The rights for each role are restricted to the user languages the user selected during the registration process Sec 2 1 Register or in Preferences in the menu bar Sec 5 2 User languages amp ontologies 7 2 1 Term Editors Term Editors are the users of VB with the most restricted editing rights They are usually terminologists by background Term Editors may access to the following modules e Recent changes e Concepts e Export In the Concepts module Term Editors may perform the following actions VB 2 0 User Manual Page 47 of 101 e Add edit and delete terms e Add edit and delete relations between terms and any other piece of information for terms e Add edit and delete concepts e Add edit and delete relations between concepts and any other piece of information for concepts All actions performed by a Term Editor get either the status Revised or Proposed depending of the action undertaken and need to be approved by a Validator 7 2 2 Ontology Editor
55. italized Proposed elements IM Deprecated Roles in workflow Capitalized Validator Term Editor Concepts terms relations Bold amp italic genetically modified organisms attributes produces HasTermType Note that all examples are taken from the AGROVOC concept scheme VB 2 0 User Manual Page 9 of 101 1 Introduction VocBenchi VB is a web based multilingual vocabulary management tool developed and hosted by a collaboration between the Food and Agriculture Organization FAO of the United Nations the University of Rome Tor Vergata and the Malaysian research centre MIMOS Berhad VB supports the maintenance of SKOS RDF resources providing support for workflow and editorial processes such as user rights roles validation and versioning that are associated with the development and management of vocabularies VB is adopted by a growing number of user communities including FAO s multilingual agricultural thesaurus AGROVOC gt FAO s Fisheries and Aquaculture Department and the data fao org project the European Commission Publications Office the European Environment Agency the Italian Senate and others This manual refers to version 2 0 released in November 2013 and is the result of a joint effort between FAO and the ART Artificial Intelligence Research group of Tor Vergata In its 2 0 version VB met the objective of enabling a quicker dataset independent setup and providing a collaborative platform for the managem
56. l Geographical below country level Fishery related term Add Cancel Figure 37 Advanced search Search for Fishery related term 6 2 7 Search for term attribute Terms may be specified by attributes For example Figure 38 shows the list of attributes currently available for AGROVOC terms Click on the icon in the Term attribute field to open the list and select the desired term attribute e g use HasTermType to find concepts whose terms belong to a specific subvocabulary VB 2 0 User Manual Page 42 of 101 of terms Select term attribute Relationship None None agrontology hasPlural agrontology hasSingular agrontology hasTermType agrontology hasSpelling Variant Figure 38 Advanced Search Search for term attribute A new field Value is added select here the subvocabulary you want to search in e g Common name for plants Figure 39 and click on Add Select term attribute Relationship agrontology hasTermType Value Acronym y Acronym Common name for animals Common name for bacteria Common name for fungi Common name for plants Common name for viruses Taxonomic terms for animals Taxonomic terms for bacteria Taxonomic terms for fungi Taxonomic terms for plants Taxonomic terms for viruses Figure 39 Advanced Search Search for Common name for plants 6 3 Concept navigation history The orange button Concept navigation history in the botto
57. lick on Add Figure 5 select language Arabic Bengall Al Bosnian L Catalan Czech Danish German Greek Spanish Also known as Farsi Finnish Fijian French Hindi 4 Canes Figure 5 Select language VB 2 0 User Manual Page 14 of 101 Note It is important to make a distinction between settings that determine the languages you want to use for concept search and visualization and settings that determine in which languages you want to edit concepts The languages you select in the registration form are the ones which you would like to use for editing To use other languages to search for concepts click in the top right corner of the VB user interface on the orange box Content language Figure 11 C and select the language s which you would like to use for concept search and visualization see Sec 3 1 4 Concept navigation history amp Content language e Select ontology box Click on the sign select from the drop down list the ontology ies you wish to manage or contribute to and click on Add Figure 6 Select ontology adaqravoc faotopics Add Cancel Figure 6 Select ontology 3 At the bottom of the form there is space for comments 4 After clicking the Save button a message appears confirming your registration Figure 7 VB 2 0 User Manual Page 15 of 101 You have been registered please check your email for further details Figure 7 Registration confirmation
58. m of the search area Figure 40 gives you a chronological overview of the concepts navigated during your current session indicating date and time Figure 41 VB 2 0 User Manual Page 43 of 101 Exact word A Go Advan search Figure 40 Search area Concept navigation history Concept navigation history O 2014 03 17 12 12 48 ie MOND de Moon en Luna es Lune fr Luna it O 2014 03 17 12 12 46 rA MODELL de Models en Modelos es Mod le fr Mod le d exploitation fr Modelli it O 2014 03 17 12 12 32 el FOSSIL de Fossils en F siles es Fossile fr Fossili it O 2014 03 17 12 07 34 ioi PRIVATDARLEHEN de Private loans en Pr stamos privados es Pr t prive fr Prestiti privati it 2014 03 17 11 13 52 0 Heide de Heideland de Moorland de heathland en moorland en moors en Brenal es Landas es P ramos es Tierra yerma es Brande fr Lande fr Brughiere it Landa it Territorio di brughiera it 9 2014 03 17 11 13 32 ii Habitat de habitats en Habitat es Sitio ecol gico es Habitat fr Habitat it 2014 03 17 11 13 14 Figure 41 Concept navigation history 6 4 Content language The orange button Content language in the bottom of the search area Figure 40 gives the option to select the languages you would like to search and visualize concepts in The languages you select here are only related to searching and visualizi
59. m the drop down list e g Proposed or Deprecated Figure 35 and click on the Search button Status All All Classification scheme Proposed by guest Proposed Concept attribute Revised by quest Revised Proposed deprecated Term attribute Deprecated Validated Published Deleted Figure 35 Advanced search Search for status Proposed deprecated 6 2 5 Search for concept scheme Use this option to select the scheme you want to search in 6 2 6 Search for concept attribute Use this search option to find for example concepts belonging to a specific subvocabulary of concepts Figure 36 Click on the icon to open the list and select the desired concept attribute e g Is part of subvocabulary VB 2 0 User Manual Select concept attribute Helationship agrontology isPartOfSubvocabulary agrontalogy isSpatiallylncludedinCity agrontology isHoldBy skos scopeNote skos note skos editorialHote skos example skos changeNote skos historyNote Figure 36 Advanced search Search for concept attribute Page 41 of 101 Example Search for a fishery related term Figure 37 After selecting Is part of subvocabulary from the drop down list a new window opens in which you may select Fishery related term Select concept attribute Relationship agrontology isPartOfsubvocabulary v value Chemicals T Chemicals Geographical country level Geographical above country leve
60. me with or without its children The format of export is SKOS XL format Recent changes Concepts Relationships Schemes validation Load data Statistics Upon entering the Export module you may specify your export using the following three fields Figure 99 Export Schemes Select v Concept None i CDhetude children Format SKOS XL v Oude labels of related concepts se zip compression Export Figure 99 Export module e Schemes Click on the dropdown box and select the scheme to export If you want to export only one or few concepts from that scheme specify that in the Concept field below e Concept To select the concept to export click on Browse A window opens containing the top concepts of the scheme Figure 100 you selected in the Schemes field Here you have the possibility to include or exclude for faster export the children of the selected concept by checking the children checkbox Figure 99 VB 2 0 User Manual Page 92 of 101 e Format By default SKOS XL 2 You can decide to include or exclude for faster export the labels of related concepts Note In the bottom left corner you may want to check the Use zip compression to save time and space Concept browser Exact word y 5 Reload concept Ls activities en rey entities en ra events en E il factors en E la features en G groups en A location en amp ra measure en la metho
61. ng and only for the current session In Preferences you may set the languages in which you would like to edit concepts see Sec 5 2 User languages amp ontologies Note To visualize the terms of a concept in all languages the check box Show only terms of selected languages should be unchecked If on the other hand you check this box you will only be able to view the terms in the languages you selected VB 2 0 User Manual Select languages to display Use this area to select languages you wish to see when viewing concepts categories and relationships and to use in searching in your current session By default in every next login the content language will be setto the users languages All the changes in the content language will be valid for the current session only You will always see only in user languages when viewing terms associated with concepts and categories To see in all the language use the preferences area to check Show also non selected languages under Administration attop ofthe page Add new language Order T AB 43 38 13 40 19 49 1 15 32 Language arabic Elara bosanski jezik catal cesky E dansk deutsch E EMrvIKa english espa ol persian iT Select all Clear all Figure 42 Content language Note arabic bengali bosnian danish german greek english spanish also Known as farsi finnish Code ar l bn A bs ar
62. on Figure 96 VB 2 0 User Manual Page 88 of 101 Validation filter Filter by user Filter by action Filter by status Administrator A concept create E _ Proposed by guest andrea concept delete _ Proposed arterisk concept editrelationship create Revised by quest _ atifah concept edit relationship edit Revised avoc Uk concept editrelationship delete Proposed deprecated beikzadeh term create Validated bingyan term edit bramangkoun tenm delete caracciolo term relationship add cklee75 tenm relationship edit O O Filter by date erystalwying tenm relationship delete LJ Today cwbong term note create _ This Week Dister term note edit This Month dlukose term note delete edenizaslani term attribute create From DD MM Y Y YY ehesse i term attribute edit v m A DDMMYYYY term attribute delete t Clear Date Figure 96 Validation filter 1 Filter by user By default all registered users are unselected To validate changes by specific users simply check the check box in front of their name To select all users check the All box at the bottom of the list to unselect all users click the All box again Note These settings will be saved also for your next sessions 2 Filter by action By default all possible actions are unselected To select actions simply check the appropriate check boxes
63. onfirm it in the next field e Ontology In case you are an editor of more than one ontology you may state here which ontology you would like to be loaded by default e Set your landing Page To set the VB module you want to visualize after logging in e Language of the interface From the drop down list you may select the language in which you would like to visualize the VB interface Note Currently the user interface is available in English default Spanish Dutch and Thai e Show URI By default the URIs of concepts are not displayed This check box corresponds to the check box Show URI in the Concepts module valid for the current session only e Show also non preferred terms By default only the preferred terms are displayed To see also the non preferred terms check this box VB 2 0 User Manual Page 29 of 101 Note The box corresponds to the check box Show also non preferred terms available in the Concepts module Show only terms of selected languages The terms you see displayed in the concept box under the Terms tab are by default shown in all available languages If you check this box only terms in the selected languages are shown see 5 2 Hide deprecated terms and concepts By selecting this option the concept hierarchy will show only concepts and terms with the following status Proposed Validated Published Revised For detailed information about statuses in VB see Sec 7 2 User roles Show inferre
64. ou are looking at You may narrow the time span down by using the options in the Filter by date box To apply the filter click on Submit Filter by user Filter by action Filter by date Administrator concept create Today andrea concept delete This Week arterisk concept edit relationship create This Month atifah concept edit relationship edit From DD MM YYYY avoc Uk concept edit relationship delete beikzadeh term create To DD MM YYYY bingyan term edit bramangkoun term delete caracciolo term relationship add cklee75 term relationship edit crystalwying term relationship delete cwbong term note create Dister term note edit dlukose term note delete edenizaslani term attribute create ehesse term attribute e dit GJohannsen term attribute delete GRFFNPII OT 02 concent edit note create Clear Date Page size 15 Submit Cancel Figure 46 Recent changes filter VB 2 0 User Manual Page 53 of 101 9 Concepts module The Concepts module is available to all roles It is used to e Browse and navigate the hierarchy of concepts e View the information attached to the individual concepts and terms e Add edit delete concepts and terms This section is divided into two parts the first part is dedicated to operations on concepts the second one to operations on terms 9 1 Operations on concepts A concept is anything that is relevant in a given domain A concept is represented by all terms preferred and non preferred and in
65. ou to the newly created concept area where you may create other preferred or non preferred terms in other languages by clicking on Add new term see Sec 9 2 1 Add a new term 9 1 3 Delete a concept This action may be performed by Editors Validators Publishers and Administrators 1 Select the concept in the concept hierarchy 2 Click on the icon in the bar above the concept hierarchy 3 A warning message is visualized Figure 61 4 Follow the instruction when ready click Delete VB 2 0 User Manual Page 66 of 101 Delete concept ATTENTION You are about to delete a concept with all its associated terms new child concept en all its subconcepts and all its relations to and from other concepts Before deleting this concept please make sure that all its sub concepts if any are deleted or moved under a new parent Also make sure that all its relations are to be deleted The new status of the deleted concept will be draft deprecated Delete Cancel Figure 61 Delete concept Warning message Note When you delete a concept its status becomes Proposed Deprecated meaning it only becomes deprecated after it has been approved by a Validator or Publisher see Sec 7 2 User roles In the meantime its terms in all languages do not change status 9 1 4 Edit the information attached to a concept This action may be performed by Term Editors Ontology Editors Validators Publishers and A
66. posed Accept Reject l Accept all L Reject al The validation table contains the following information options in eleven columns 1 Concept Term Relationship Users Note mM Validate VB 2 0 User Manual Page 87 of 101 10 11 Shows the concept when the change belonged to the concept e g the creation of new concept a new term a new concept to concept relationship Shows the term when you add any term term relationship Change shows the current value of the element Old value shows the previous value of the element Action indicates the action applied to the element Owner shows the owner of the element Modifier indicates by whom the change was performed Creation date shows when the element was created Modified date indicates when the change was applied Status shows the current status of the element Validate option to accept or reject the modification Note Here you may enter a comment regarding the validation The comment is automatically sent to the modifier 12 1 Validation filter You may filter the list of validation actions presented in the Validation table There is an Apply filter option at the top right of the Validation module Figure 95 The filter functionality is very useful when there is a long list of issues to be validated Clicking on Apply filter a window opens showing the following specific filter options to facilitate the selection for validati
67. r URL Figure 9 Login Add ontology project It is also possible to remove an ontology from the list select the ontology you wish to delete and click on the sign VB 2 0 User Manual Page 17 of 101 3 User interface The language of the user interface for VB is currently available in English default Spanish Dutch and Thai Note You have to decide the language of the user interface on the VB entry page i e the page where you login to access the VB user interface It is a small drop down box at the top right corner of the VB entry page Figure 1 The VB user interface is organized into two different areas Figure 10 1 The menu area Figure 10 I Menu This area is organized into three horizontal menu bars o General settings top menu bar Figure 10 A o Search central menu bar Figure 10 B O Access to different modules bottom menu bar Figure 10 C 2 The content area Figure 10 IIl Content displays the module you selected VB 2 0 User Manual Page 18 of 101 Signed in as Johannsen Administrator to agrovoc Administration AboutVocBench RSS feed C Preferences Help Sign out LA VERSION 2 0 Build 20131025 Recent changes Relationships Schemes Validation Load data Export Statistics Concepts 2 aktivity cs Aktivit t de activities en actividades es activit fr Attivit it Aktiviti ms etkinlik tr ninrieHicre uk 25 3 zh E celky
68. r rcu A PR e EAE ENEE NERENS ENERET REEERE ETENEE 37 0 23 SOUTO term CODES o AAN Dae eee ear 39 6 2 4 Search TOF STATUS xoi eese aeta tu ea Ra Pe sa cU eaa rebos fu ea pv veo uda vada ta due eb pn sae COTON vao cra o dE dE 40 5 2 9 SENEN TOF CONCEDES CNE O ie na ote Pan fie en D fuera pe dad aon obe emu EL A A AA 40 62 6 Seareh TOF CONCE DE att adas 40 6 2 ZSeurch JOPterm ait iDUte SS AA AA Die Dep dc ES 41 6 3 CONCEPT NAVIGATION HISTORIA Ene CAP Da UE EM D M AL 42 6A CONTE NIT LAIN GUAGE scm ORE ERR ER UR FU Utm ds e E LO UN MEM EM a I M MEE 43 7EDITORIALWORKFLOW ec 45 HESIATUS OE TERMS AND CONCEPT S c Tv PnM 45 Ti 2 USER ROLES Cr rn 46 Fa MET ea TO IA T A A e 46 Te ZZ OntolOD ENC OMS scissors os epus uns CO sas ounce coon sass MIL CO MM M TDI IM M CMM M TIE IU IM UL oca 47 FS MONA O DOES ta tc 48 EL Gy PUNSET Ei Ea 48 Zeo AAMI OTO RR A E 49 8 RECENT CHANGES MODULE sisi 50 S TANPPISCEIBEERSOPTIONS S ora Mond tasas ie E M MEM lr M MM i E M I M i DE E 51 VB 2 0 User Manual Page 3 of 101 9 CONCEPTSMODULE siio xuE a lada 53 PASO PE RATIONS ON CONCEPTS i cues deii Ae LEM e ELA Ei a a ELLA EL EE 53 UA O ETE 54 LL AO A new concept ut cte ep A A cE ta skate ebsncbsieanes 63 91 3 Delete ICON CO uin uui ed ardet E autos tup deed ausi eso eoo tet ue A A doi e LU Ue eR A 65 9 1 4 Edit the information attached to a concept 0 0 ccccccecccccsseccccesccccuseccc
69. ral machinery industry en o ry Appliances en Equipment en Implements en x Agricultural machinery industry en iR Produces en Installations en Instruments en Machinery en Machinery industry en Tools en m rey Alcoholic beverages en al Alcoholic fermentation en Ethylic fermentation en R Produces en G Ethanol en Ethyl alcohol en I O Allium ampeloprasum en Allium porrum en R Produces en e Leeks en Oj Allium ascalonicum en R Produces en le Shallots en ra Allium cepa en R Produces en rey Onions en Spring onions en Oj Allium fistulosum en R Produces en ig Japanese bunching onions en Welsh onions en ry Allium sativum en R Produces en y garlic en lO Allium schoenoprasum en R Produces en G chives en iG Amanita en R Produces en G Amanitin en ig American cranberry en Vaccinium macrocarpon en R Produces en G Cranberries en 44 1019 Figure 30 Results of Advanced search Search by relation 6 2 2 Search by both relation AND concept Type in the search box the word you want to search for select in the Relationship browser the relation you are interested in as described above and click on the Search button Figure 31 shows a search for preferred terms only by word virus AND by relation Causes The results are displayed in Figure 32 VB 2 0 User Manual Page 38 of 101 Exact word Advanced search options
70. rea The relation area is organized in tabs Figure 84 Each tab provides access to a different piece of information about the selected relation For example Figure 84 shows the Label tab for the relation has narrower IRI skos narrower Label 1 English has narrower Figure 84 Relationships area Tabs The following other tabs are available IRI skos narrower Definition 1 Language Definition English Narrower concepts are typically rendered as children in a concept hierarchy tree Figure 85 Relationships area Definition tab IR skos related Properties SymmetricProperty Figure 86 Relationship area Property tab VB 2 0 User Manual Page 81 of 101 IR skos narrower Inverse Property 1 Inverse Property R has broader en Figure 87 Relationship area Inverse property IR skos narrower Domains 2 amp Ranges 3 Domain owl Thing skos Concept owl Thing skos Concept node Figure 88 Relationships area Domains amp ranges tab Note Functionalities as Add Edit Delete a relationship label and Edit the information attached to a relation are not available for imported relations 10 2 Operations on relations 10 2 1 Add a new relation This action may be performed by Publishers and Administrators To add a new relation take the following steps 1 Choose where in the hierarchy to add the new relation VB 2 0 User Manual Page 82 of 101 2
71. referred NJ ra site en G stages en uj state en Bahasa Melayu ms organisma W ra strategies en G subjects en substances en ra systems en LG Technics en technology en Pycckuii ru opraHnu3mbl Preferred NJ Deutsch de Lebewesen Preferred W7 1 time en K Legend Proposed W Validated Bil Published Bill Revised Mi Proposed deprecated Bill Deprecated Show more oe FAO 2011 Figure 49 Concept hierarchy area A and Concept term area B Concept hierarchy area A Starting from the left there are a number of buttons with the following functionalities Figure 50 VB 2 0 User Manual Page 57 of 101 ais Concepts MEE Validation Concepts 2 amp EE t ht v Sho up E Showa preferred URI http aims fao org aos agrovoc c 331061 le activities en la entities en lc events en LE le factors en ra groups en tg oL T eX te ra location en lc measure en Figure 50 Buttons on concept hierarchy area e Reload concept Refreshes the screen and reloads the selected concept or the entire hierarchy if no concept is selected al e Collapse all This tab collapses the concept or all the concepts when its hierarchy is being expanded e Add new concept To add a new concept to the hierarchy e Delete concept To delete the selected concept TT e Move concept To move the selected concept e Link concept E To link th
72. relationships field VB 2 0 User Manual Page 39 of 101 6 2 3 Search for term codes Terms have codes which are shown in the Notation tab of the Term box If you know the code of a term you may use the Term codes field to search for the concept to which the term is related In Figure 33 you can see the term codes currently available in AGROVOC In order to search for a concept with a given term code select the Repository e g skos notation Figure 33 enter the code in the Code search box e g 7698 Figure 34 and click on Search Advanced search options Repository None Search in these language s 2 4 Term codes None Code agrontology hasCodeTaxonomic English agrontology hasCodelSO3Country Hindi Status AN agrontology hasCodeF aoterm Telugu agrontology hasCodeAsc skos notation agrontology hasCodeFishery3Alpha agrontology hasCodeFaoPa Concept scheme Select Concept relationships agrontology hasCodeAsfa Term relationships Concept attribute Term attribute Figure 33 Advanced search Search for term codes Select repository Repository skos notation Y Term codes Code 7698 Figure 34 Advanced search Search for term code VB 2 0 User Manual Page 40 of 101 6 2 4 Search for status This option allows you to retrieve all terms concepts having the selected status see Sec 7 1 Status of terms and concepts In order to use this search option select the term concept status fro
73. rty Figure 78 Example of object properties for AGROVOC e Datatype properties Data type properties relate objects to data type values so that the value of the corresponding RDF triple is a literal value e g a string Relationships Datatype properties Y Show URI R xsd minExclusive R xsd mininclusive R xsd maxLenath R agrontology hasSingular R xsd length R xsd maxinclusive Figure 79 Example of Datatype properties for AGROVOC e Annotation properties 11 Steven J Miller Introduction to Ontology Concepts and Terminology VB 2 0 User Manual Page 78 of 101 Annotation properties may be used to annotate any entity e g owl versionInfo rdfs label rdfs comment No range is defined for these properties Relationships Annotation properties v a rdfs seeAlso R owldeprecated R rafs label R owl priorversion skos note IRI owl backwardCompatiblev vith R owl versionInfo IRI owl incompatiblevyith rdfs comment Figure 80 Example of Annotation properties for AGROVOC e Ontology properties Ontology properties relate two ontologies their domain and range must be an owl Ontology Relationships Ontology properties Show URI BR owv imports B owl backw ardCompatibleVvith BB owlincompatiblewvith Be owl prior version Figure 81 Example of Ontology properties for AGROVOC 10 1 User interface The Relationships module displays the relations of the type selected in the
74. s Ontology Editors are more experienced terminologists and thesaurus editors and have all the rights of Term Editors Ontology Editors have access to the following VB modules e Recent changes e Concepts e Export e Statistics In the Concepts module Ontology Editors may perform the following e Add edit and delete terms e Add edit and delete relations between terms and any other piece of information for terms e Add edit delete concepts e Add edit and delete relations between concepts and any other piece of information for concepts All actions performed by an Ontology Editor get either the status Revised or Proposed depending of the action undertaken and need to be approved by a Validator VB 2 0 User Manual Page 48 of 101 7 2 3 Validators Validators are experts that can check and validate the work done by Term Editors and Ontology Editors Validators have all the rights of Term Editors and Ontology Editors Validators may access the following modules of VB e Recent changes e Concepts e Validation e Export e Statistics In the Concepts module Validators may perform all actions also allowed to Term Editors and Ontology Editors In the Validation module Validators may accept or reject any action that has been proposed or by Term and Ontology Editors Those items then get the status Validated or Deprecated in the case of the status Proposed deprecated 7 2 4 Publishers Publishers
75. s MUA ats DH E ESTIS Scheme Validation Load data Export Statistics Figure 16 Menu area C Access to content Module bar e Recent changes All roles VB 2 0 User Manual Page 22 of 101 Lists recent changes applied to VB such as modifications applied to terms and concepts user registrations etc see Sec 8 Recent changes module e Concepts All roles This module is divided into two panels The left side of the screen shows the browsable concept hierarchy of the concept scheme ontology you selected when you logged in or you selected in the module Schemes see Sec 11 Schemes module the right side visualizes the concept you selected including its terms relationships etc This module is used to add edit delete concepts terms relationships etc see Sec 9 Concepts module e Schemes Administrator To add or remove concept schemes Note The scheme selected here is the one displayed in the Concepts module see Sec 11 Schemes module e Relationships Administrator amp Publisher Shows all the relations available for use in the ontology together with their definitions This module is used to manage relations The actual instances of relationships are visualized in the Concepts module see Sec 9 Concepts module e Validation Administrator Publisher amp Validator Shows all proposed changes applied to the concept scheme to be validated see Sec 12 Validation module e Load Data Administr
76. sary of Biotechnology for Food and Agriculture FAQ 2001 http www fao org DOCREP 004 Y 2775E y2T75e00 htm en skos editorialNote Figure 53 Concept term area Note e Attribute Shows the available attributes for the selected concept Figure 54 Gl Asia en Attribute 1 Add new attributes Attributes Value Is part of subvocabulary 9 Geographical above country level Figure 54 Concept term area Attribute e Relationship Shows the relations between the selected concept and other concepts Figure 55 le genetic drift en Add new relationship Relationship Concepts Influences en 2 gene frequency en allele frequency en Figure 55 Concept term area Relationship e History VB 2 0 User Manual Page 62 of 101 Shows the history of the selected concept Figure 56 Creation date of concept Date of last update Term status 2 Detailed information on term changes Note This information is automatically generated E genetic drift en Term 1 Definition 1 Note 0 Attribute 0 Relationship 1 j Image 0 Hierarchy Creation date 1998 09 04 00 00 00 Last update 2011 09 28 19 10 17 Status Published Change Old value Action User Date concept edit ext sour Johannsen 29 09 2011 13 10 Figure 56 Concept term area History e Image Shows an image of the concept e Hierarchy Presents in a compact way the hierarchy line from the selected concept
77. ser login Oo Forgot your username or password 4 Create an account Figure 2 User login VB 2 0 User Manual Page 12 of 101 2 1 Register Once you have clicked on Create an account the system will take you to the User Registration form Figure 3 User registration form User Registration Login name Password Confirm password First name Last name Email Affiliation Contact Address Postal code Country URL Work phone Mobile phone Chat Select Chat Types Groups you wish to register for Languages you wish to manage Ontology you wish to manage Comment Max 255 Characters Mandatory field Save Cancel Figure 3 User registration form 1 Fill in the fields Note The fields marked with an asterisk are mandatory 2 Select the groups you wish to register for and the languages and ontologies you wish to manage or contribute to e Select group box Click on the sign and select from the dropdown list the appropriate group s then click on Add Figure 4 Note To select more than one group keep the Ctrl key pressed whilst you click on the groups of your choice VB 2 0 User Manual Page 13 of 101 select group Publisher Validator Ontology editors Term editors Figure 4 Select user group e Select language box Click on the sign select from the dropdown list the language s in which you wish to edit data then c
78. sts the languages you requested access to Figure 23 to edit data in these languages e User ontology This box lists the ontologies or datasets you already have access to Figure 23 If you want to remove an ontology select the appropriate ontology and click the button If you want to request managerial rights over a new ontology click on the icon select the available ontology and click on Add The selected ontology will then be added to Pending ontology requests The VB Administrator will receive an email about the ontology request After approval you will be notified by email e Pending ontology requests This box shows the ontologies you requested access to VB 2 0 User Manual Page 31 of 101 6 Search Search functionalities are always available to all users VB allows you to perform a simple search and an advanced search Both are case insensitive Note The search results are based on your language settings In Preferences you may set the languages in which you would like to edit concepts see Sec 5 2 User languages amp ontologies these same languages are then by default used to search and visualize concepts To use other languages to search for concepts click in the top right corner of the VB user interface on the orange box Content language Figure 11 C and select the language s which you would like to use for concept search and visualization see Sec 3 1 4 Concept navigation history amp Content lang
79. ties for AGROVOC Relationships user interface Relationships buttons Relationships area Tabs Relationships area Definition tab Relationship area Property tab Relationship area Inverse property Relationships area Domains amp ranges tab Create new relation Delete relation Schemes module Scheme management Schemes Module checked scheme Schemes module Functionalities Add scheme Validation module Validation filter Refresh validation list Load data module Export module Figure 100 Export module Top concepts of selected scheme Page 6 of 101 70 70 71 72 72 73 73 74 74 75 75 76 77 77 78 78 79 79 80 80 80 81 81 82 82 84 84 85 85 86 88 89 90 91 92 VB 2 0 User Manual Page 7 of 101 Figure 101 Statistics module Select the required group 93 Figure 102 Search option Stats on concepts terms languages 94 Figure 103 Search option Stats on the structure 95 Figure 104 Search option Stats on relations and properties 95 Figure 105 option Stats on Agrovoc specific relations and properties 96 Figure 106 Option on Stats on workflow 97 Figure 107 SPARQL querying VB 99 VB 2 0 User Manual Page 8 of 101 Legend GUI elements button field Click on Add module form box names Click on the sign Go to the Select language box VB message uu the message Concept already exists Activation of your account on VocBench Status of approval of VB Cap
80. uage only valid during your current session Note Last Results make reference displays the results of your last search Note All examples are coming from the AGROVOC scheme 6 1 Simple search erecta N You may choose one of the following search options Figure 24 Exact word maize Go Advanced search Last result Exact match Contains Concept navigation history Content language starts with Ends with Figure 24 Search options e Exact word default With this option you will retrieve the concepts labelled by terms in the languages you selected matching exactly the word typed in VB 2 0 User Manual Page 32 of 101 Example Figure 25 shows the results of a search for Solanum in this example English is the only language selected VERSION 2 0 Build 20131025 Voc Bench I Solanum Advanced search Recent changes Mode Relationships Schemes Validation Load data Export X Statistics Concept navigation history Con Search results Concept Last update date Ney European potato plant en Solanum tuberosum en 29 08 2013 23 08 18 r3 egg plant en eggplant en Solanum melongena en 29 08 2013 23 08 18 rey Lycopersicon esculentum en Lycopersicon lycopersicum en Solanum lycopersicum en tomato plant en 29 08 2013 23 08 18 Ul Solanum en 20 11 2011 21 24 22 un Solanum aethiopicum en 20 11 2011 22 02 29 ry Solanum nigrum en 20 11 2011 22 02 29 r Solanum berthaultii en 2
81. uk Ll skupiny cs Gruppe de groups en grupos es groupe fr gruppi it Grupo pt rpynnbt ru eyocres te grup tr rpynn uk v Legend Proposed Bl Validated MB Published M Revised Proposed deprecated B Deprecated Show more o Figure 10 VB user interface Concepts module menu I and content area II 3 1 Menu area Signed in as Johannsen Administrator to agrovoc v Administration AboutVocBench A RSSfeed Preferences Help Sign out CA VERSION 2 0 Build 20131025 VocBench Exact word Recent changes Relationships Schemes Validation Load data Export Statistics Figure 11 VB user interface Menu area 3 1 1 General settings The top bar in the menu area marked A in Figure 11 is dedicated to the following general settings e User name Figure 12 1 Signed in as Shows the account name you used for login e Role Figure 12 2 VB 2 0 User Manual Page 19 of 101 Shows the role in brackets you selected when you logged in e g Term Editor see Sec 7 2 User roles e Dataset Figure 12 3 Shows the dataset currently in use e g AGROVOC To change to another dataset click on the arrow and select the desired one from the dropdown box 3 2 Signed in ag User peti i ciministrator Voc B enc h VERSION 2 0 teilen Figure 12 General settings User name 1 User role 2 Dataset 3 e Administration Figure 13
82. w w fao org landandwater s Js Wh http w w w fao org landandwater s Wh s Wu http www w fao org landandwater s Wu Figure 91 Schemes module Scheme management Note Only one scheme at a time may be displayed in the Concepts module Check in the Schemes module the box of the scheme you want to work with search in Figure 92 Scheme Management Select Y http aims fao org aos agrovoc Figure 92 Schemes Module checked scheme This module contains three buttons with the following functionalities Figure 93 e Reload schemes To refresh the screen e Add a new concept scheme VB 2 0 User Manual Page 85 of 101 e Delete a concept scheme Scheme URI http aims fao org aos agrovoc Op Figure 93 Schemes module Functionalities 11 1 Add a new concept scheme 1 To add a new concept scheme click on in the top right corner of the screen Figure 93 2 Add the Scheme URI the Scheme Label and select the Scheme language from the dropdown box Figure 94 Note Labels may be added only in the languages for which you have editing rights 3 Click Submit or Cancel Scheme URI Scheme label Scheme language Select Figure 94 Add scheme Once you created the new scheme it is added to the list of available schemes VB 2 0 User Manual 12 Validation module Page 86 of 101 The Validation module is available to Validators Publishers and Administrators only The module visualizes all the re

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