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INDEX BASICS: How is the Tox-Hub page organized ? 1.1. The administrator’s login area

INDEX BASICS: How is the Tox-Hub page organized ? 1.1. The administrator’s login area 1.2. Tabs bar area Heroic website Give us feedback Clean up Retrieve session DB list IUPAC toxicology glossary 1.3. Searching facilities area Search Words Search Scope Select Dictionary

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INDEX BASICS: How is the Tox-Hub page organized ? 1.1. The administrator’s login area

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  1. INDEX • BASICS: HowistheTox-Hub page organized ? • 1.1. Theadministrator’sloginarea • 1.2. Tabs bar area • Heroicwebsite • Giveusfeedback • Clean up • Retrievesession • DB list • IUPAC toxicologyglossary • 1.3. Searchingfacilitiesarea • SearchWords • SearchScope • SelectDictionary • Operateon sets • 1.4. Query sets area • 1.5. Resultsdisplayarea • GETTING STARTED: searchingwords in theTox-Hub • 2.1. Howdoesthesystemwork? • 2.2. Thewordsearchprocess • 2.3. Logicaloperations • TRAINING MATERIAL • END Returntoslide of origin Returnto MAIN INDEX NEXT SLIDE: CLICK MOUSE or USE Keyboard ARROWS

  2. HowistheTox-Hub page organized ? Tabs bar Area AdministratorsloginArea SearchingfacilitiesArea ResultsdisplayArea Query Sets Area

  3. TheAdministratorsloginAreaisspecificallyreservedforthesystem’s manager loginforinternalmaintenance and administrationtasks . Itis NOT accesible tothe USER

  4. TheTabs bar contains7 buttonshighlightedbypointingthe mouse and activable byclickingon:

  5. TheTabs bar contains7 buttonsactivable byclickingon: IUPAC Glossary: displaysthecontents of IUPAC GLOSSARY OF TERMS USED IN TOXICOLOGY, 2nd EDITION - IUPAC RECOMMENDATIONS 2007 DB List: displaysthelist of externaldatabasesaccessiblefromToxHub and provides a short informationprofile Heroicwebsite: directstothe HEROIC mainwebpage Clean up: cleans up the page tostart a new session Retrievesession: opens a dialogwindowallowingtoretrieve a previoussession Help: displaysthehelpmenu Giveusfeedback: opens an e-mail addressedtofeedback@heroic-toxhub-platform.estofacilitatesendingcommentstotheTox-Hubsystemadministrator.

  6. DB List: displaysthelist of externaldatabasesaccessiblefromToxHub and provides a short informationprofile

  7. In Built-in (YES / NO) indicatesifthetermappears in theinternaldictionary and thusifit has any link (reference) totheexternalDBs IUPAC Glossary: displaysthecontents of IUPAC GLOSSARY OF TERMS USED IN TOXICOLOGY, 2nd EDITION - IUPAC RECOMMENDATIONS 2007 http://sis.nlm.nih.gov/enviro/iupacglossary/frontmatter.html In Built-in (YES / NO) indicatesifthetermappears in theinternaldictionary and thusifit has any link totheeexternalDBs (reference)

  8. Giveusfeedback: opens an e-mail addressedtofeedback@heroic-toxhub-platform.estofacilitatesendingcommentstotheTox-Hubsystemadministrator.

  9. Retrievesession: opens a dialogwindowallowingtoretrieve a previoussession InsertdesiredUser #

  10. SearchingfacilitiesAreacontains4actionwindows: • SelectSearchscope: dropdownmenuallowingchoice of thesearchdomain (‘Title’or ‘Wholedocument’) • Selectdictionary: dropdownmenuallowingchosingtheworddictionary (‘Internalbuilt-in’or ‘IUPAC’). • Words of thedictionary: allowstoinsert a wordforsearching. Onwriting a sting a dropdownmenuappearsshowingtheavailablewords in thedictionarycontainingit. Once thewordisselectedthequeryisperformedbyclickingthe ‘GO‘ button. • Operateon sets : allowstheoperation of previouslygenerated sets usingbooleanlogicaloperators (‘AND’, ‘OR’, ‘AND NOT’). Afterselection of sets and logicalopertorsfromthecorrespondingdropdownmenus, theoperationisexecutedbyclickingthe ‘DO‘ button.

  11. SearchingFacilitiesArea Selectwords

  12. SearchingFacilitiesArea Selectscope

  13. SearchingFacilitiesArea Selectdictionary

  14. SearchingFacilitiesArea Operateon sets Selectoperator (AND, OR, AND NOT) Select Sets

  15. Query Sets Area: • Query sets generatedeitherbydirectsearchorbyapplication of logicaloperations are listedsequentially. • Sets are identifiedby: • anordernumber (1,2,…n) • a figure indicatingthenumber of hits (references) • thewordorlogicaloperationusedtogeneratethequery. • Referencescontained in any set are diplayedbyclickingSee#button • Any set can bydeletedbyclickingtherightmostbutton

  16. Query Sets Area Word orlogicaloperation use to define the set Deletingbuttons SET number and displaybutton Number of ‘hits’ (links toexternalDBs) found

  17. ResultsdisplayArea: • References (hits) obtained in theselectedquery set are displayed • Thefollowinginformationisshown: • Link totheExternal DB itiscomingfrom • Name of theExternal DB • Indicationifthewordiscontained in thetitle. • References are paginated in blocks of 10

  18. ResultsdisplayArea NUMBER of REFERENCES PAGINATION (blocks of 10) SET # LINK toexternal DB (accesible byclicking) NAME OF EXTERNAL DB Title of thedocument (ifthewordappears)

  19. Howdoesthesystemwork? • Tox-Hub is an internet based information platform designed to facilitating the user the simultaneous access to some external toxicological databases. • External databases are periodically scanned, their contents analyzed and the relevant words extracted and stored together with the link address to the original database. • Such pairs word/reference are contained in the Tox-Hub internal database and constitute the core of the system. • This task, performed prior to the user intervention, allows collecting relevant words and locates the address (web-link) where the word was originally taken from. • Original references can be retrieved and accessed through the web after a suitable searching process.

  20. The word search process When performing a search the user must specify three information fields: • Searching scope: Title or Full document (referred to the original external databases). • Remark: currently only the option ‘full document’ is available. ‘Title’ search will be soon activated. • Dictionary: referred to the internally automatically generated (built in) dictionary, or alternatively, to the use of an external one. • Remarks: • At this moment only one external dictionary is available (IUPAC). • Unlike the internal built dictionary, not all the words contained in an external dictionary may fit the external databases and are thus not usable. For instance the IUPAC dictionary contains ca. 1517 terms of which only 625 are usable. Note that only usable words appear in the dropdown list. • Words: specific keywords related to the topic of interest should be selected.

  21. The word search process • Words available to the user are displayed by typing on the input field. • On writing a string, a dropdown list of words containing it is displayed. While continuous typing the list is automatically updated and shortened(Google-like) • Remark: at the beginning of the process a default list of words appears. At starting of writing it is automatically actualized. Alternatively, the default list can be deleted by clicking the ESC key • Any word appearing in the list has at least one reference. • Remark: the list of words in the dropdown display can be empty. That means that there is no external reference fitting these words. • The user can choose any word by direct clicking it or by up down displacement using keyboard arrows followed by a return. The pointed word is highlighted in red. • Remark: a word not appearing in the menu is likely due to two possible reasons: • - The word does not appear in any of the external databases available. • The word is covered (substituted) by a term belonging to the same family (ex.: ecotoxicity, ecotoxic are considered the same). • Once the word is selected, it is fixed in the searching box. • The searching process is launched by clicking the GO button.

  22. The word search process After launching the searching process, a set fulfilling the query specifications is generated. Any set contains a number of references (at least 1) in which the keyword is contained. The set generated is added in the Query Sets Area Set contents (references) are listed in the Results Display Area. They are paginated and displayable in blocks of 10. From every retrieved reference (web-link) it is possible to access the original information (located in the original external database) by simply clicking the link.

  23. The word search process • New searches using different keywords can be issued in the same session and the corresponding sets are saved (stored in an intermediate memory) for further use. Every Set generated is characterized by the corresponding keyword. • Combining these keywords can be done by using logical operations between pairs of sets. • Logical operations require filling the Operate on sets field, located in the Searching Facilities Area: • Select sets • Select logical operator (AND, OR, AND NOT) • Click DO button • Query sets generatedeitherbydirectsearchorbyapplication of logicaloperations are listedsequentially in theQuery Sets Area • Display of references in the Results Display Area of any set previously generated can be achieved by clicking on the See button.

  24. Logical operations • To perform logical operations we obviously need at least two built sets containing the correponding words & references. • To specify an operation the three dropdown lists placed beneath the input box. The first and the third dropdown show the list of the sets available for the operation and the second dropdown display shows the kinds of operators that are available. These operators are AND, OR and AND NOT. • Logicaloperations can berecursivelyappliedtoevery new generated set • Logicaloperationsbetween sets are bettervisualizedusingVenn-Eulerdiagrams

  25. Logical operations Example: we wish to retrieve references containing the terms ‘bioactivity’ and ‘toxicity’. First we proceed to build separately the corresponding sets with the two words selected: Set #1: ‘bioactivity’ (4 references) Set #2: ‘toxicity’ (641 references) Secondly the logical operations can be performed. The set #1 is selected in the first dropdown, the operator AND is selected in the second and the set # 2 is selected in the third dropdown selector. In the example, both sets have 4 common references and this new generated set ise designated as set #3 'bioactivity' AND ' toxicity ‘ Set #3: ‘bioactivity’ AND ‘toxicity’ (1 AND 2) (4 references) Following with our example, the results of applying the other logical operations to set #1 and set #2 are: Set #4: ‘bioactivity’ OR ‘toxicity’ (1 OR 2) (641 references) Set #5: ‘bioactivity’ AND NOT ‘toxicity’ (1 AND NOT 2) (0 references) Set #6: ‘toxicity’ AND NOT ‘bioactivity’ (2 AND NOT 1) (637 references)

  26. Set #1: ‘bioactivity’

  27. Set #2: ‘toxicity’

  28. Set #1 AND Set #2: ‘bioactivity’ AND ‘toxicity

  29. DifferentLogicaloperationsappliedto • Set #1: ‘bioactivity’ • Set #2: ‘toxicity

  30. Representation of thelogicaloperationsusingVenn-Eulerdiagrams

  31. Training Material (in construction)

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