Handling URL Links on Web Diagrams

Transcription

1 Handling URL Links on Web Diagrams Xiao Mang Shou, Siobhán North Abstract This report describes the design and development of a technique of handling URL links on diagrams within a diagram database which forms a part of the Cytokine WebFacts database as well as other text documents and images. The underlying diagram database is constructed based on a Web application which allows geographically distributed users to contribute new and modify existing diagrams directly and interactively on the Web. To provide broader information within the Web diagrams, those diagrams need to be linked to relevant Web pages inside or outside the Cytokine WebFacts database. Due to the distributed nature of Web users, it is neither practical nor secure to let each user to be aware of the structure of the whole database in order to make the URL links. Instead, a new method has been designed to provide a tool for users to select the relevant URL links directly on the Web according to a document description and embed them into diagrams. It is a new approach for easier, securer and more friendly URL handling on Web diagrams. 1. INTRODUCTION URL links is one of the prominent features of the WWW. Basically, URL links within text based documents can be easily achieved through HTML whereas URL links in images are usually pursued through imagemaps. A typical example of imagemap used in bioinformatics is the SWISS-2DPAGE map selections [Swiss00]. Imagemap is the most common method for addressing URL links within non text information, such as complicated tables [Tumor00], graphs [Yeast00A] and sketch drawings [Yeast00C]. For most diagrams on the Web today, they are either isolated diagrams without URL links ([Bridge97], [Barghouti98]), or they are treated the same way as images ([CSNDB00], [Yeast00B]) and URL links are addressed on the diagrams the same way as within imagemaps. However, it is not wise to store the Cytokine WebFacts diagrams as imagemaps in order to impose URL links within them. This is not only because imagemaps would occupy too much storage space and slow down the network traffic, but also because those diagrams are based on the current state of scientific understanding in cytokine research which is a rapidly advancing field. Those diagrams are bound to change frequently as new cytokine signal pathways and methods are discovered. Therefore, they should not be treated as static images. The Cytokine WebFacts diagrams are edited and submitted by geographically distributed users all over the world using the WIDE (WWW Interactive Diagram Editor) [Shou99] tool. The ability to handle URL links is one of the points which differentiate the Cytokine WebFacts diagrams from conventional diagrams. Though there are some other kinds of editable Web diagrams such as Grappa [Barghouti98] and GDS [Bridge97], they do not support URL links on their diagrams. The original idea of adding URL links within the diagrams comes from the requirement that some text in the diagrams needs to link to other Web pages, or even other diagrams. 1

2 Because of the nature of URL links, Cytokine WebFacts diagrams are not as flat and static as ordinary diagrams, though they may have the same appearance. Through the URL links, Cytokine WebFacts diagrams can have much broader and more dynamic content. The concept of handling URL links within the Cytokine WebFacts diagrams is also different from the conventional idea that URL links are predefined by the webmaster where users are completely not involved. Since the Cytokine WebFacts diagrams are constructed based on user submissions, users are entitled to submit new diagrams and modify existing diagrams in the database directly. This means users play a much active role in building and maintaining the diagram database. To be consistent with the active roles of users in diagram editing, the URL links within the diagrams are also allowed to be added, removed or updated directly by users. In a previous prototype of the WIDE diagram editor, URL links were entered by mouse clicking over the text. A pop up window would be shown as the follows to allow the entry of the URL address directly: Fig 1. URL address input window From this pop up window, a user could enter any URL address freely, but only a valid URL address would be accepted and assigned to the specified text. There are some disadvantages for using this method: 1. First of all, if a user want to link text to a file of Cytokine WebFacts database, he/she must know the exact path and file names in the server in order to make a valid link. For example, in order to link text IL1 with its home page, users need to know the exact directory /cytokine/il1/ and the file name IL1.html on the server. It may not be a problem for the webmaster to do so, but it is not realistic to expect other users from all over the world to have the same knowledge, let alone that the server structure and files are supposed to be hidden from outside users for security reasons. This will significantly restrict users from making related links within the Cytokine WebFacts server. Although users can type in other URL addresses which are not on this server, it is estimated that the majority of the links will still point to the local cytokine files on the server. 2. Users have to follow up the updates of the Cytokine WebFacts server all the time in order to make valid URL links. Those updates can be, for example, new files or directories added to the server, file names and directory names changed, or even the server changed to another address or port, etc.. Since 2

3 these kinds of updates are likely to happen quite often, it is unrealistic to request all external users to catch up. 3. Users cannot have an overview of all available links. They probably will only stick to the few web pages they know while there may be other more relevant links around. It relies completely on how familiar users are with the server structure and files. 4. It is almost impossible for users to make links to other Cytokine WebFacts diagrams as the diagram storage and maintenance on the server is completely hidden from the end users for security reasons. 5. It is tedious and error prone to have to type in the full URL address every time. In order to solve this problem, it is necessary to provide users with the most relevant URL link automatically. It is possible to automatically fill in the pop up window with the IL1 home page URL when users click on IL1 within the diagram editor, so that users do not need to know about the file paths and file names on server. However, there are major problems with this method: it is not always easy to determine the most relevant URL because users are entitled to add URL links on any text they like freely. Besides, for users who want to link IL1 text to the IL1 home page, the detailed URL address provided which consists of the directories and the real file name on the web server is not very meaningful, they still need to know the directory structure of the web server in order to determine whether it is the correct link or not. To avoid the above problems associated with URL links in Cytokine WebFacts diagrams, ideally there could be a friendly interface via which users can make URL links easily, flexibly and freely without being aware of the internal server structure. Under these circumstances, the idea of having a URL selection list for users to select a URL link rather than entering it themselves was established. 2. DESIGN OD THE INTERFACE The interface of the URL selection list for Cytokine WebFacts diagrams evolved through several stages. Initially, the URL selection list was designed as Fig 2 to list all cytokine home pages which link to web pages containing all attributes of a specific cytokine. The description of each cytokine file was shown in the select list so that user can have a better understanding of the selections and do not need to know about the real URL address. The real URL address of the selected web page would be shown at the bottom text field. In order to give users the freedom to make URL links, users were allowed to enter the URL link directly on the text field as well. If there was already a URL link assigned to the text, the original value of the URL address would be shown in the text field for users to update. Whatever the case, the final value shown in the text field would be used for the real URL address. The selections provided in this interface were the 50 cytokine types. 3

4 Fig 2. Selections for cytokine home pages Using this method, a specific cytokine type can only link to its home page which contains all its attributes. Since every cytokine type within the Cytokine WebFacts has information under the same 18 attribute headings such as the cytokine s crossreactivity, bioassays, amino acid sequence, etc., some of the text within the diagrams may need to link to a specific attribute, it would be more flexible to let users choose from all available attribute files rather than only providing them with the home page of all attributes. Thus, the interface of the URL selections was then modified as the following: Fig 3. Selections for cytokine attributes Using this interface, the selection list displayed the brief description of each attribute instead of real file names as it was more descriptive. In this selection list, the available selection items were the 18 cytokine attribute files. Users could choose any attribute of the specific cytokine type freely. The home page containing all attributes was also provided within the selections as the item all attributes. The cytokine type of which the attributes were listed was dynamically determined by the text that user selected to address the URL link. For instance, if user clicked IL1 text, then all IL1 attributes were listed. Though this design provided more choices of attributes, it restricted those attributes to those belonging to one specific cytokine type. It had the 4

5 advantage of eliminating unrelated URLs by only providing the most relevant selections. But very often, the text to be assigned a URL link is not a cytokine type, in that case it is difficult to determine which cytokine type should be used. Furthermore, it is also common for the same text to link to different cytokine types, there are still too few choices to select by using this method. It is more flexible to integrate the previous two designs and give the users all available cytokine links to select freely, regardless of the chosen text. Therefore, the interface was updated as the follows: Fig 4. Selections for both cytokine types and attributes In this design, there were two columns of selections, one for cytokine types and the other for cytokine attributes. The content of the attribute column is decided directly by the cytokine type selected in the first column. For example, if IL2 is selected in the left column, all IL2 attributes will be listed in the right column for selection. As before, there was also an all attributes item included in the attribute column for all cytokine types to link to the web page which contains all cytokine attributes. The final URL will be set automatically according to the selection made in the attributes list, or otherwise entered directly in the text field. Combining the two columns together, there were cytokine type x cytokine attributes = 50 x 18 = 900 choices which covered all available cytokine files on the Cytokine WebFacts server. The advantage of this design was that users could have a complete view of all available links in the web server and select freely among them. Furthermore, it was more practical as all available links were provided every time no matter what the chosen text was. The chance of mistakes in selecting the correct URL could be reduced by setting the default value in the selection lists. For text already linked to the Cytokine WebFacts files, the originally selected values were set in both the cytokine type and attribute columns. If there was no link assigned before, the default cytokine type was selected according to the given text and the all attributes item would be selected in the attribute column as default. If the text was linked to an external URL which did not belong to the Cytokine WebFacts, no default value would be set, but the existing value would be shown in the bottom text field. In any case, the bottom text field would always display the current URL value, users could update it without any restriction. 5

6 The primary drawback of this design was that it was repetitive to generate the attributes list every time the user made a selection in the cytokine type column. This procedure is necessary when each cytokine is summarised into different attribute headings. Since all cytokines in the Cytokine WebFacts server share the same attribute headings, it would be simpler to list all the attribute headings in the right column and combine the values in both selection lists for the final URL address. So far the URL selections had covered all available cytokine files of the server, but this was not sufficient. Parallel with the text information, cytokine signal pathway diagrams themselves are another kind of data of the Cytokine WebFacts database. An outstanding feature of the Cytokine WebFacts diagrams is that they can be linked with each other as well as text files. To provide a wider choice in URL links, diagrams should also be included in the selections. Unlike cytokine files, diagrams are not clearly classified into different types and attributes. To offer better support for users to select the correct diagram, the diagrams must be represented by their summary information such as title, keywords, and description. Considering the keywords and description are not as brief and clear as the title, in order to use the same interface as the cytokine files, diagrams could be presented by their titles in the right column, and the left column would be left blank. When using the available prototype of the Cytokine WebFacts diagram editor WIDE to add URL links, there was another problem that occurred frequently which was the repetitive appliance of the same URL link. In many cases the same URL link has to be applied to multiple same text strings within the diagram. For example, if there are 5 "IL6" strings in the diagram, it is usual that they all need to link to the same URL address. To achieve this, the same procedure of selecting URL had to be performed 5 times. This repetition could be avoid by adding a function to apply the URL link to all the identical text strings. Since there are also occasions that same text string may link to different URL address, the function to apply the URL to specific text only must also be reserved. The final interface of the URL selection is shown in Figs 5 and 6. It has the categories of "Cytokine files", "Diagrams" and "Other". "Other" category is reserved for future expansion and has not utilised yet. Both the cytokine type and attribute column are empty in Other category. Two buttons, "Apply to all matching text" and "Only to this text" have been added at the bottom to apply the specified URL to all the identical text strings within the diagram or apply the URL to the chosen text only. 6

7 Fig 5. The interface of URL slections in Cytokine files category Fig 6. The interface of URL slections in Diagrams category The above interface can be used to add new URL links or update existing URL links within Cytokine WebFacts diagrams. Once the URL links are assigned, it is also important to have the ability to remove them. Though it is possible to remove URL links by leaving the real URL text field empty, but this is not clear and direct. Therefore, a reminder window shown in Fig 7 is designed to pop up right after the user selects the text. The URL selection window will pop up after the Assign new/update existing URL button is pressed. 7

8 Fig 7. The reminder window for URL selections Since there is the function to apply the same URL link to all matching text strings within the diagram, it is natural to have the function to remove URL links from all the matching text strings to avoid the repetitive operation. Another reminder window shown in Fig 8 will pop up after the Remove current URL button is clicked. Fig 8. The reminder window for removing URL links 3. DEVELOPMENT AND IMPLEMENTATION Once the interface was designed, the problem remaining was retrieving the real URL address according to the selected items in the lists, for both cytokine files and diagrams. Under the Cytokine files category, there are different ways to list cytokine types and attributes. Ideally, this information can be loaded automatically and dynamically by a program traversing the Cytokine WebFacts server. As cytokines are stored individually in the server, each cytokine has its own directory under the server s document root directory. It is possible to list cytokine types by retrieving all those sub directory names dynamically every time the URL selection list is generated. The advantage for using this method is that the cytokine types listed in the selection list will always be the most up-to-date available ones. However, since not all the directories under the document root belong to cytokines, there must be another mechanism to distinguish which are the valid ones. In cases where there are changes such as the addition of new or renaming of old directories, or a change in the server directory structure, this kind of mechanism are probably need to be re-examined to make sure it catches up with the updates. Since the changes of server documents and 8

9 structure are likely to happen quite often, this kind of re-examination may occur frequently. Furthermore, retrieving the cytokine types dynamically may be too repetitive and waste a lot of system resources. Compared to the changes in server directories, cytokine types are much more stable. It is not necessary to refresh the selection list every time it is loaded. The cytokine types can be fixed in the left column, or more flexibly, can be read from an external file which can be modified easily when new cytokines are found. For attributes, though it could be possible to get attribute headings by retrieving the <title> field in HTML files under the individual cytokine directory, it is not practical to do so because those HTML files could vary a lot, some of them may not even have the <title> field. There may be files unrelated to the cytokine attributes stored in the same directory as well. More important, as discussed before, because the same 18 attribute headings are used for each cytokine, they also can be fixed in the right selection column, or read from an external file. The cytokine type selected in the left column is used to identify the directory in the server and the attribute selected in right column is used to locate the real file name. Handling URL links within diagrams is related to the problem of determining the cytokine type based on the given text. For text which does not belong to any of the cytokine types, it is unrealistic and not practical to find the matching cytokine type. However, often the user may use different names of the same cytokine type, or type the cytokine type in another format. For example, IL1 can also be presented as IL- 1, Interleukin 1, IAF, EP, LEM, etc.. Ideally the URL selection tool will be intelligent enough to recognise them as the same as IL1. To achieve this intelligent response, there must be a file storing the alias information of all cytokine types. This file can be used as a filter to decide the real cytokine type name. In this file, each cytokine entry is represented by a formal name with multiple equal weight, format unlimited alias names. Only the formal names will be displayed in the cytokine type selection list are used to identify the directory name in the server. Since this kind of information is changed frequently when new alias names are assigned, or when new entries are added, this alias file is stored as an external file which can be updated freely at any time without affecting the whole system. Another benefit of using this alias file is, the WIDE program can use it to get all the cytokine formal names to display in the left selection column without hard coding, or dynamically reading the directories in the server. It is much easier and more flexible for modifications. To improve the speed and efficiency of the whole system, this cytokine name alias file is loaded into a data structure in the programs when system initialisation so that cytokine type verification can be done by referring to the data structure rather than open the external alias file every time. Retrieving the real file name from the selection made in the attributes column requires a translation mechanism to reflect each attribute description to the corresponding file name in the server. Since the default value needs to be set according to the existing URL link, this translation mechanism must be reversible to be able to relate the file name to its attribute description. Another external alias file similar to the cytokine type alias file holding the information of all attribute description and corresponding filenames can be created. The attribute description in this file is read to be displayed in the right selection column by WIDE programs. This external file can also be 9

10 updated freely by the webmaster at any time for future modification and maintenance. Like the cytokine name alias file, this file is also loaded to a data structure in the programs when initialising the system. Currently, cytokine signal pathway diagrams are loaded through URL links pointing to the corresponding diagram data files. Those diagram data files are stored under the same directory on server with the.dat extension. Under the Diagram category of the URL selection list, the major task is to list all diagram titles in the right selection column and to build a scheme to reflect the selected diagram title to the corresponding diagram data file. A complete search of the diagram database must be performed for this task. The procedure of retrieving diagram titles from data files is similar to the diagram search engine which goes through the diagram directory to search every data file. This work has to be done by a Java servlet as it needs to list all data files under a server directory. Meanwhile, a data structure must also be designed to hold the diagram titles and the corresponding data files to record the connection between them. Instead of launching the Java servlet to perform a search every time diagram URL selections are requested, it is much quicker and more efficient to perform the search once when starting the system to initialise the data structure and then use this data structure ever after. In the whole WIDE system, most of the global and dynamic parameters, such as the URL root of the programs and servlets, the URL root of the Cytokine WebFacts documents, the data path of the diagram data files, the URL root of the external initial files, etc. are all specified as the applet parameters in the external HTML files which load the WIDE applet. All those parameters can be changed easily and freely without touching the WIDE source code. This gives the maximum flexibility for deploying, updating and maintaining the WIDE system. The WIDE URL selection list was implemented in Java with a Java servlet on the Java Web Server to retrieve diagram titles and data file names. It has been tested and obtained satisfactory result. It is quicker, easier, clearer, more user friendly and more flexible to manipulate URL links within the Cytokine WebFacts diagrams. The whole structure of the Cytokine WebFacts diagram URL selection list is shown as the follows in Fig 9: 10

11 Text selected in WIDE diagram Cytokine alias names filter URL selection list Category? Cytokine file Diagram Cytokine type Cytokine attribute Diagram title Attribute filter Title filter Cytokine file name Diagram data file name Generate real URL address Generate real URL address Final URL address Fig 9. Process of handling URL selections of WIDE diagram 4. DISCUSSION AND FUTURE WORK Once the URL selection list has been built for Cytokine WebFacts diagrams, it raises the problem of version control of the diagram database. At present, all WIDE diagrams are stored under the same directory on server, all those data files are regarded as available to be listed in the URL selection board. While the user is editing the diagram, new diagrams may be saved on server to be available for URL selections. As described earlier, the current implementation of WIDE does not have the mechanism to dynamically refresh the URL selection. However, such a mechanism is not critical, it can be achieved by adding the similar refresh or reload functionality without technical difficulties. To prevent users from updating the diagram database freely, there will be different directories to store the diagrams. New or updated diagrams will be saved on provisional directories with the provisional file names first to be checked by domain 11

12 experts, and only authorised diagrams will be moved to the permanent database. In view of the fact that the future permanent database may be classified into different directories, diagrams in all those directories should be included into the selection list as well. This can be done by specifying the corresponding parameters in the HTML files loading the WIDE applet. Another problem of the URL selection list is caused by the function of applying/removing URLs to/from all identical text strings. The most common situation is, after applying the URL to all identical text strings, user may enter another identical text string. Will this text be automatically linked to the same URL address or not? Though, in most cases the text string will link to the same URL, there are still occasions when a different URL link may assigned, or no URL link may assigned. When clicking the text to assign a URL link, it is possible to remind the user whether the same URL has been assigned to other identical strings and check whether this text string should be assigned the same URL automatically, but this requires a thorough search and comparison of all matching text strings hence would significantly slow down the system. Right now, applying the old URL address to newly entered text string can be done by reselecting the URL again in the selection list, or by performing the Applying to all Matching Text function again, none of these methods are as tedious as reminding user to assign the same URL automatically. Therefore this reminding function is not yet developed. When doing the Removing URL from all Matching Text function, it is also possible that the identical text strings are assigned with different URL links. It would be ideal to remind the user about this circumstance before removing them. However, this function will also require a thorough search and comparison of all matching text strings and so it was not developed either. The applying/removing URL to/from all identical text strings functions needs to determine which strings should be counted as identical. In the current version of WIDE, identical strings are those who are exactly the same, case sensitively. For cytokine type strings, it is not difficult to consider all the alias names as identical, and it is also easy to ignore the case in comparison. However, in some cases those alias strings would link to different URL pages, it may caused further problems to regard them as identical and apply/remove URL links to/from them together. As a result, this function is so far reserved. During the design stage of the WIDE URL selection list, the possibility of opening a display window to show the content of the current selection was considered. For example, if a user selected a text URL link, the display window would show that text file. Respectively, if a diagram URL selection was made, the specified diagram would be shown in the display window. This method would provide direct and visual comprehension to help the user making the right choice and technically speaking, there is no critical problems in implementation. Nevertheless, loading the text HTML file or the diagram into the display window every time a selection was made could significantly slow down the whole system, especially as users are supposed to switch among the selections many times before a final choice is made. Besides, the display window may cause confusions to novice users. Therefore, this function was not developed either but it can be added in future. In the current implementation of WIDE, the URL selection list for Other category is left empty. The Other category is reserved for providing URL selections other than 12

13 cytokine files and signal pathway diagrams, such as related links in other web sites, related documents, etc. It is very useful to include this category in order to provide wider range of URL selections. Handling Other URL selections can be similar as handling cytokine file and diagram selections. An external text file can be built to store the information of web page summary descriptions and corresponding URL addresses. The summarise description will be listed in the right column and the real URL address of the selected item will be display on the bottom text field. For future expansion of the system, those Other URL links can also be classified into different types such as related researches, related publications, etc. Because one web site/page can belong to multiple classified types, a relational table holding the classified types, web page summarised descriptions and the URL addresses can be created with the summarised description as the primary key. This table can be stored in an external file and can be updated easily as well. By reading this external file, classified types can be listed in the left selection column and the descriptions belonging to the selected type can be displayed in the right selection column dynamically. Combining them together, the WIDE URL selection list can offer a much broader range of selection. The updating of the external files which holds the information of classified types, web page descriptions and URL addresses can be done by the webmaster or domain experts. To enhance the system flexibility, users can be allowed to update these files directly and automatically by submitting the relevant information to the system through certain interface on the Web. Again, this method may come across problems such as repeated submission, invalid data, etc.. To ensure that the external file contains reasonable information only, the webmaster or domain experts can verify user submissions and only the correct information is entered in the external file. Because there are not enough related URL links provided by the domain experts at present, this function is not implemented and can be developed in the future. After implementing the functions to apply/remove URL links to WIDE diagrams, it is necessary to be able to undo these functions as in other editing modes. There is no technical problems to achieve this but as this function is not critical to the system and due to the limited time, it is not implemented and can be developed in the future as well. 5. CONCLUSION The ability of handling URL links within diagrams is a significant feature of the Cytokine WebFacts diagrams and the one which is different from other sorts of diagrams. The URL links provides flexible and simple access from diagrams to other kind of information, including other diagrams. Therefore, Cytokine WebFacts diagrams can have much wider and more dynamic contents. When dealing with the URL links within the Cytokine WebFacts diagrams, users need not passively follow the URL links predefined by the webmaster as in most other Web applications, they are offered the full freedom to add, remove and update URL links to any text objects in the diagram as they require. They are much more involved in manipulating URL links in Web diagrams. 13

14 In early versions of WIDE, the URL links within diagrams were entered one by one manually. It required users to be familiar with the server s directory structure and the file names stored on the server. This was neither practical nor safe. Besides, it was tedious and repetitious to input the URL address manually. To avoid these disadvantages, the URL selection list was developed to provide an easy, navigated and friendly method for users to select and apply URL links within diagrams. Unlike ordinary selection lists are, the items available in the WIDE URL selection list are not hard coded. They were loaded to the selection list by reading from external files which stored the document summary information of the server files. Those external files can be updated freely at any time to offer the maximum flexibility for URL selections whenever there were any modifications on the server. Furthermore, the URL selection list utilised the document directory structure in the Cytokine WebFacts server when generating the real URL addresses dynamically according to user selections. Therefore, the URL selection list is not isolated from the Cytokine WebFacts server, it integrated the server files and directory structure to provide the flexible, dynamic and easily updated selections for WIDE diagrams. All the related parameters used in URL selection list were parsed through external files which can be modified easily so this tool can be plugged into other Web servers with different settings without difficulty. The WIDE URL selection list offered URL selections of WIDE diagrams as well as the cytokine files on the server. It is also possible for it to collect the selections in other Web sites from users. Under this mechanism, users can contribute new URL links to the server to be listed in the selection list. The webmaster can check the submitted links to ensure only valid and relevant links are listed. Through this method, users play a more active role in maintaining and modifying the URL links within Cytokine WebFacts diagrams. Other useful functions like applying/removing the URL link to/from all matching text strings have also been implemented. Acknowledgement: This work is partially supported by Academic Press. REFERENCE [Bridge97] S Bridgeman, A Garg and R Tamassia; A Graph Drawing And Translation Service on the WWW ; Graph Drawing, Lecture Notes in Computer Science (1190); Springer-Verlag; 1997; p45-52 [Barghouti98] N S Barghouti, J M Mocenigo and W Lee; Grappa: A GRAPh PAckage in Java ; Graph Drawing, Lecture Notes in Computer Science (1353); Springer-Verlag; 1998; p Last accessed: February 2000 [Shou99] Xiao Mang Shou, Siobhán North; WIDE: A WWW Interactive Diagram Editor ; Proceedings of the First International Conference on 14

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