INDEX 1.BASICS: How is the Tox-Hub page organized ?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 Operate on sets 1.4. Query sets area 1.5. Results display area 2.GETTING STARTED: searching words in the Tox-HubGETTING STARTED: searching words in the Tox-Hub 2.1. How does the system work? 2.2. The word search process 2.3. Logical operations 3.TRAINING MATERIALTRAINING MATERIAL 4.ENDEND Return to slide of origin Return to MAIN INDEX NEXT SLIDE: CLICK MOUSE or USE Keyboard ARROWS

How is the Tox-Hub page organized ? Administrators login Area Searching facilities Area Query Sets Area Results display Area Tabs bar Area

The Administrators login Area is specifically reserved for the system’s manager login for internal maintenance and administration tasks. It is NOT accesible to the USER

The Tabs bar contains 7 buttons highlighted by pointing the mouse and activable by clicking on:

The Tabs bar contains 7 buttons activable by clicking on: Heroic website: directs to the HEROIC main webpage Give us feedback: opens an addressed to to facilitate sending comments to the Tox-Hub system Clean up: cleans up the page to start a new session Retrieve session: opens a dialog window allowing to retrieve a previous session Help: displays the help menu DB List: displays the list of external databases accessible from Tox Hub and provides a short information profile IUPAC Glossary: displays the contents of IUPAC GLOSSARY OF TERMS USED IN TOXICOLOGY, 2 nd EDITION - IUPAC RECOMMENDATIONS 2007

DB List: displays the list of external databases accessible from Tox Hub and provides a short information profile

IUPAC Glossary: displays the contents of IUPAC GLOSSARY OF TERMS USED IN TOXICOLOGY, 2 nd EDITION - IUPAC RECOMMENDATIONS ter.html In Built-in (YES / NO) indicates if the term appears in the internal dictionary and thus if it has any link to the eexternal DBs (reference) In Built-in (YES / NO) indicates if the term appears in the internal dictionary and thus if it has any link (reference) to the external DBs

Give us feedback: opens an addressed to to facilitate sending comments to the Tox-Hub system administrator.

Retrieve session: opens a dialog window allowing to retrieve a previous session Insert desired User #

Searching facilities Area contains 4 action windows: Select Search scope: drop down menu allowing choice of the search domain (‘Title’ or ‘Whole document’) Select dictionary: drop down menu allowing chosing the word dictionary (‘Internal built-in’ or ‘IUPAC’). Words of the dictionary: allows to insert a word for searching. On writing a sting a drop down menu appears showing the available words in the dictionary containing it. Once the word is selected the query is performed by clicking the ‘GO‘ button. Operate on sets : allows the operation of previously generated sets using boolean logical operators (‘AND’, ‘OR’, ‘AND NOT’). After selection of sets and logical opertors from the corresponding drop down menus, the operation is executed by clicking the ‘DO‘ button.

Select words Searching Facilities Area

Select scope Searching Facilities Area

Select dictionary Searching Facilities Area

Operate on sets Select operator (AND, OR, AND NOT) Select Sets

Query Sets Area: Query sets generated either by direct search or by application of logical operations are listed sequentially. Sets are identified by: an order number (1,2,…n) a figure indicating the number of hits (references) the word or logical operation used to generate the query. References contained in any set are diplayed by clicking See # button Any set can by deleted by clicking the rightmost button

Query Sets Area SET number and display button Deleting buttons Number of ‘hits’ (links to external DBs) found Word or logical operation use to define the set

Results display Area: References (hits) obtained in the selected query set are displayed The following information is shown: Link to the External DB it is coming from Name of the External DB Indication if the word is contained in the title. References are paginated in blocks of 10

Results display Area NUMBER of REFERENCES PAGINATION (blocks of 10) SET # LINK to external DB (accesible by clicking) NAME OF EXTERNAL DB Title of the document (if the word appears)

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. How does the system work?

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).Searching scope 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.Dictionary Remarks: 1.At this moment only one external dictionary is available (IUPAC).IUPAC 2.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 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.Words:

The word search process Words available 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.GO

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 AreaQuery Sets Area Set contents (references) are listed in the Results Display Area. They are paginated and displayable in blocks of 10.Results Display Area 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.

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:Operate on sets Searching Facilities Area - Select sets - Select logical operator (AND, OR, AND NOT) - Click DO buttonDO Query sets generated either by direct search or by application of logical operations are listed sequentially in the Query Sets AreaQuery Sets Area Display of references in the Results Display Area of any set previously generated can be achieved by clicking on the See button.See

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. Logical operations can be recursively applied to every new generated set Logical operations between sets are better visualized using Venn-Euler diagramsVenn-Euler diagrams

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’Set #1: ‘bioactivity’(4 references) Set #2: ‘toxicity’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’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’Set #4: ‘bioactivity’ OR ‘toxicity’(1 OR 2)(641 references) Set #5: ‘bioactivity’ AND NOT ‘toxicity’Set #5: ‘bioactivity’ AND NOT ‘toxicity’(1 AND NOT 2)(0 references) Set #6: ‘toxicity’ AND NOT ‘bioactivitySet #6: ‘toxicity’ AND NOT ‘bioactivity’(2 AND NOT 1)(637 references)

Set #1: ‘bioactivity’

Set #2: ‘toxicity’

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

Different Logical operations applied to Set #1: ‘bioactivity’ Set #2: ‘toxicity

Representation of the logical operations using Venn-Euler diagrams

Training Material (in construction)