INDEX 1. BASICS: How is the Tox-Hub page organized ?

1.1. The administrator’s login area1.2. Tabs bar area

Heroic websiteGive us feedbackClean upRetrieve sessionDB listIUPAC toxicology glossary

1.3. Searching facilities areaSearch WordsSearch ScopeSelect DictionaryOperate on sets

1.4. Query sets area1.5. Results display area

2. GETTING STARTED: searching words in the Tox-Hub2.1. How does the system work?2.2. The word search process2.3. Logical operations

3. TRAINING MATERIAL4. END

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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 e-mail addressed to feedback@heroic-toxhub-platform.es to facilitate sending comments to the Tox-Hub system administrator.

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, 2nd 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, 2nd EDITION - IUPAC RECOMMENDATIONS 2007 http://sis.nlm.nih.gov/enviro/iupacglossary/frontmatter.htmlIn 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 e-mail addressed to feedback@heroic-toxhub-platform.es 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

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 fromName of the External DBIndication if the word is contained in the title.

• References are paginated in blocks of 10

Results display Area

NUMBER of REFERENCESPAGINATION (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).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: 1. At this moment only one external dictionary is available (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. 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.

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.

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.

The word search processNew 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 generated either by direct search or by application of logical operations are listed sequentially in the Query Sets Area

Display of references in the Results Display Area of any set previously generated can be achieved by clicking on the See button.

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 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’ (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)

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)