Data entry application for NMS partners User manual
Contents
1. ear of publicatic In another possible example the Original title and English title fields accommodate titles of a conference paper while into a Book title field a conference proceedings title should go Pages field is meant for the paper s from to numbers and not for the proceedings collation Similarly complex situation occurs with the authorship data With the same form the names of chapter authors and the names of book editors have to be entered The different roles of these persons are marked with values from the drop down list as in Figure 24 Book chapter conference paper analytic Netscape Book chapter conference paper analytic creator jure IBMI creation date 27 10 2004 document ID 912 updated 13 10 2004 Author s affiliation Author s email LOOSS Author s affiliation Cana Author s type Co Booo Author s type editor Author s affiliatior CO DD Author s email PO rdinal position of author Authors affiliation Author s email Irdinal position of author Figure 24 Entering data about the authors of a book chapter and the editors of a book that contains this chapter by using the same data entry form The overall characteristics of this data entry form is that it lacks the fields which are normally intended for physical characteristics of a printed document i e pages 23 volume collation2. gt https unimed mf uni lj si Eureth net data entry Mozilla Firefox oj x Eureth net data entry user jure Record ID 1638 was entered changed euroethics main authors uncontrolled terms Thes Ethics Life Sci MeSH database euroethics gt primary document type journal article gt new record close Figure 6 Confirmation of successful transfer and writing of record into a database If the user is entering new record the submit button would send it to the server and reset button would forget changes or do nothing if the form is empty If the user realises that s he doesn t want to create a new record the close button will end the data entry session without sending anything to the server To enter data about document s author s a separate data entry form has to be used A form filled with data about three authors is shown on Figure 7 This form is accessible by pressing the authors button after the main data were submitted or after the search was successfully performed Authority is a complex information Besides the authors names two other non mandatory pieces of data is expected by Documentary standards author s affiliation and author s e mail address According to Standards only the 1 author s affiliation and address is to be entered but quite often it is not the 1 author of a document that the mail has to be sent to therefore the application enables the us
3. Eureth net searching Netscape i 15 x Pu nik D Management kot kadrovska funkcija na podro ju zdravstvene nege 0 In Lahe M Kau i BM editors Sodobni pristopi v zdravstveni negi Zbornik predavanj s strokovnega sre anja Dru tva medicinskih sester in zdravstvenih tehnikov Maribor 2004 feb 25 Maribor Maribor Dru tvo medicinskih sester in zdravstvenih tehnikov Maribor 2004 16 8 euroethics gt main authors uncontrolled terms thesaurus ethics MeSH delete all data full record 862 NMEC RS book chapter or conference paper Verckovnik T Eti na vpra anja pri pouku biologije 0 fn Nai M editor Zbornik seminarjev Naravoslovje v estem in sedmem razredu devetletne osnovne Sole Naravoslovje v strokovnih in poklicnih in poklicnih olah Naravoslovje za otroke s posebnumi potrebami 2004 mar 20 22 Roga ka Slatina Ljubjana Zavod republike Slovenije za olstvo 2004 17 euroethics gt main authors uncontrolled terms thesaurus ethics MeSH delete all data full record 863 CECIB journal article Biesaga T Etyczne granice transplantacji Ethical limits of transplantation Studia z bioetyki 2003 1 185 196 full record 864 CECIB journal article Kraj T Eutanazja a eugenika we wsp czesnej praktyce medycznej Euthanasia and eugenics in the contemporary medical practice Studia z bioetyki 2003 1 197 221 full record Figure 17 Not all search hits could be edited In this part
4. close would close the working window and bring the starting window into focus fill the web form There are 7 different data entry forms one for each primary document type Each form consists of three types of fields text fields selection fields and checkboxes Selection fields and checkboxes are convenient ways of data entry when possible values are known in advance selection fields when only one value can be chosen i e with the country of publication field and checkboxes for multiple selections The overall design and pointers on this page are prescribed by the Eureth net web design group and are not developped with the data entry application 4 i e the language of document field Simple keyboard entering is used for text fields Some additional data is presented on each form database name username creator s name creation date document ID and date when this version of a form was introduced into the application The primary document type of a record is shown as the form s title Document ID is a unique un changeable number that this record has in the application s database Figure 3 shows the part of a typical form https unimed mf uni lj si Book chapter conference paper analytic Mozilla Firefox Original title Obravnava bolnikov z du evnimi motnjami v ambulanti splo ne nujne medicinske pomo i in ng Book title Urgentna medicina izbrana poglavja 6 Zbornik 7 mednarodni simpozij o urgentni medi
5. electronic This form is intended for documents that are born digital and have no printed document version and documents which were accessible to the indexer only in an e form For other physical documents that also have e versions use the appropriate data entry forms and fill the URL field An e document is a vaguely defined concept Its only defining characteristic is that it is readable in an e form but besides that it could be any other primary type most probably a journal article analytic or monograph The data entry form for e documents contains fields for all these document types It is the user s task to decide which fields to fill in the form because the application doesn t check whether the combination of fields entered is logical If the document is a journal newspaper article or a monograph the decision is easy besides the mandatory fields mostly fields that are under the form s subtitle Article or chapter or conference paper in the first case or under the subtitle Monograph in the second case have to be filled Again the situation is a more complex one if the e document is a chapter in a book or conference paper in conference proceedings obviously both in an e form In that case some fields from both groups of fields have to be filled and the principle is same as it was described in the case of the data entry form for an analytic document type For example the e document is a conference paper Am
6. record To delete values in fields of a new record that hasn t been submitted yet it is enough to press the reset button enter uncontrolled terms submit uncontrolled terms To enter uncontrolled terms a separate data entry form has to be used This form opens after pressing uncontrolled terms button from the data entry or search results window Besides the MeSH and Thesaurus Ethics in Life Sciences TELS descriptors the Documentary standards include several fields that could also be seen as subject description fields i e Uncontrolled terms Congress name as a subject Personal name as a subject etc The Uncontrolled terms field is meant for keywords or key phrases coming from some local thesaurus other than MeSH or TELS To simplify data entry all these fields use the same data entry form An additional field Uncontrolled term s type is introduced to the form with a selection list including values keyword personal name institutional name legal text project name and congress name see Figure 8 Each of these values corresponds to a Documentary standards field of roughly the same name e g Personal name as a subject The order of uncontrolled terms in a bibliographic record could be important Often the record creator enters more important keywords first and the keywords that describe less important subjects come later The information about the preferred order of keywords is maintained by entering their running
7. Author and uncontrolled term forms have place for the next piece of data To edit a record that was entered sometimes before it is necessary that this record is found first The searching facility should be used To change some field value in a particular record this record have to be found first A part of a data entry application is a search form that can be used to locate a record or a number of records The search form is accessible from the starting window Figure 1 The search form can be seen in Figure 16 Eureth net searching Netscape 0 x Eureth net searching user jure document ID 224 database alldatabases gt primary type alldocuments institution fallinsttutions a search string CO ee t T english title authors l uterms thes M MeSH go close Figure 16 A search form with all selection fields with the exception of the document number empty The role of this search form is exclusively the selection of records that have to be edited it is not meant to be an interface to some web search engine Search fields that are present in a form were selected with this function in mind The button go starts searching Result is a list of hits This list could be as large as the whole database if go was pressed without any search criteria or one record long if the search criterion was single document s unique identifier or any other combination of search criteria that yields only one hit
8. Mozilla Firefox To save the file press Save in case of a check Save it to disk and press OK in case of b or check Save to Disk and press OK in case of c lt record gt lt DNO22916zs lt DNO gt lt DB gt eurcethics lt DER lt CRE IPDE lt CRE lt CRD gt 20050304 lt CRD lt doctypes lt PTP2newspaper article PT P lt doctypes lt LAN POL lt LAN lt OTT Dridzns na prochachs OTI gt SETI gt A baby on drugs ETI gt lt P YR 2000 lt PYR gt lt DPU gt 2000 Mar 20 lt DPU gt lt JI l gt Gazeta Wyborczas JTI gt lt ISS 0660 908X lt TSS lt COUsPOL lt COU gt lt ISU gt 69 3370 lt ISU gt lt PAG gt 14 lt PAG gt lt DDS gt YES lt DDS gt SCOSBOUW O40406 lt 5C0 gt Sauthor gt lt AUT Eniczkowska M lt AUT lt fauthor lt THES lt IDDES 1952 lt IDDES gt lt DES pharmaceutical consumption DES THES gt lt THE gt lt IDDES 78 lt IDDE5 gt lt DES childrens DES lt THES lt record gt Figure 21 A record marked with XML style tags A record is a part of a file composed for downloading after the user pressed the XML button positioned above the search hits Viewing the XML ised records without saving them could be slightly more difficult If Internet Explorer is used as a browser then pressing Open will simply start the Internet Explorer window with a file presented in it or any other specialised XML viewer if such is already associated
9. Transplantation 3 Hematopoietic Stem Cell Transplantation Cell Transplantation 4 Bone Marrow Transplantation Cord Blood Stem Cell Transplantation Corneal Transplantation Fetal Tissue Transplantation Heart Transplantation Heart Lung Transplantation Hematopoietic Stem Cell Transplantation Islets of Langerhans Transplantation Kidney Transplantation ha up down select heading un select heading lt we Rm EEA Figure 10 The second search string transpl was used to make a new subset of MeSH and two new descriptors were selected only one of them as important By pressing the button submit the list of terms that was compiled using this data entry form is transferred to the server and saved into the database The form is closed by pressing the close button This data entry application provides no real orientation in the MeSH thesaurus It is of course much easyer to search and select the appropriate descriptors if one uses a proper MeSH browser Our advice is to open additional web browser window and load MeSH browser located at http www nlm nih gov mesh MBrowser html NLM The button Navigate from tree top on a MeSH browser s page shows thesaurus as a browsable hierarchical structure However it is not possible to transfer descriptors from NLM s MeSH browser into the data entry application If the selected MeSH term represents the subject that is particularly important for the current do
10. an existing record reset will discard all subsequent changes Data in many fields is automatically checked Checking is performed twice on the client s browser before sending the form to the server and on the server before entering the record into database Server side checking doesn t produce any message to the user while client side checking does Following are two typical messages that user have to obey in order to send the record to the server JavaScript Application X JavaScript Application X A Mandatory Field Year of publication is empty PiN Invalid integer Format in Year of publication Figure 5 Messages informing user about the actions that the application expects him to do enter the publication year in the first case and correct the data that were entered into the same field and probably contain something else beside digits in the second case After pressing OK the cursor is positioned on the field that caused the message Data is sent and the record is created in the database only if submit action succeeded The success is confirmed with a note like the one shown on Figure 6 The application is ready for entering authorship or subject description data to the record that was just created or changed use the first row of buttons on Figure 6 or creating new record with basic data set as in the previous one use the second row of buttons on Figure 6 cancel data entry enter author data
11. document s subject This string has to be entered into the Search Thesaurus Ethics in the Life Sciences field and search button has to be pressed https unimed mf uni lj si Journal article Mozilla Firefox 5 x Journal article creator jure IBMI creation date 21 03 2005 document ID 1637 updated 15 12 2004 adult stem cells a blood stem cells cells embryonic stem cells eukaryotic cells USE eukaryotes fetal stem cells germ cells primordial stem cells prokaryotic cells USE prokaryotes seminal cells USE spermatozoa somatic stem cells USE adult stem cells stem cells z I major heading up down gt select heading un select heading lt submit close Using data from Thesaurus Ethics in Life Sciences version 2004 Use regulated by the Licence Agreement Done unimed mF uni lj si 4 Figure 13 Data entry form forTELS descriptors User limited the thesaurus to terms that include the string cells The subset of TELS that includes this string was transferred with the form and placed inside the left selection list The user is free to select and transfer to the right list as many TELS terms as needed To complete the description of the document s subject several repetitions of the searching through TELS and selecting in the left selection list will probably be needed https unimed mf uni lj si Journal article Mozilla Firefox Oj
12. numbers into the field Ordinal position of uncontrolled term If by mistake the terms were not entered in the correct order it is enough to change the numbers in their ordinal position fields The correct order of data will be restored after the form is submitted W Book chapter conference paper analytic Netscape 7 Oj x Book chapter conference paper analytic creator jure IBMI creation date 09 10 2004 document ID 224 updated 27 10 2004 Uncontrolled term psychiatry g Uncontrolled term s type keyword gt emergency service j keyword gt choose one congress name institutional name keyword legal text Uncontrolled term s type patent name personal name Ordinal position of uncontrolled term project name submit reset close Figure 8 Data entry form for uncontrolled keywords The selection list with values denoting term types is shown Each time the form is opened there is place for one more uncontrolled term Pressing the button submit sends data to the server and into the database If data were successfully submitted the form with data entered so far is resent to the user s PC and the user can enter another term Button close terminates this cycle and closes the window 10 delete uncontrolled terms enter MeSH terms The uncontrolled term cannot be submitted to the database without entering values in Uncontrolled term s type an
13. Documentary standards expect different format but in the data entry form more human readable date format is used The date format that actually enters the database is Documentary standards compliant send data field name serves as a hypertext pointer Clicking on the field name opens new window with the text clarifying rules or possible problems regarding the data entry of this field see Figure 4 type Excerpt from the Documentary standards The original title of the document Rules Book title Edition Transcribe the title proper exactly as it appears on the work Series The title proper is separated from other titles by period space o Itis capitalized according to the original language of the document Publication place Punctuation within the title should be retained Publish snc a This field must ahways be entered Year of publication Done unimed mf uni lj si A Figure 4 Help window which opened after the user clicked on the Original title field name After the data has been entered pressing the button submit will send them to the server and if everything goes well into the database tables The role of the button reset is to forget all changes that were made since the user s PC received the form If the form was received blank the user is creating a new record reset will empty it again if the form was received filled with data the user is editing
14. Jure Dimec Brane LeskoSek Institute for Biomedical Informatics Faculty of Medicine Ljubljana Slovenia Data entry application for NMS partners User manual Ljubljana March 2005 Introduction How to enter record fill the web form send data cancel data entry enter author data submit author data delete author data enter uncontrolled terms submit uncontrolled terms delete uncontrolled terms enter MeSH terms mark MeSH terms as important delete MeSH terms set the order of MeSH terms enter terms from Thesaurus Ethics in the Life Sciences mark TELS terms as important delete TELS terms set the order of TELS terms edit existing record search for records document ID database primary type institution search string missing fields print or download records Mandatory fields creator creator date document number authors original title english title year of publication document type language thesaurus keywords Multiple occurrence fields Data entry forms analytic chapter in a monograph conference paper audiovisual material electronic document journal article newspaper article grey literature monograph OCOOMmMWoOnANA A A A Oo Introduction This user manual was written to help using the data entry application which was developed to collect the bibliographic data about publications that belong to the ethics domains covered by the Eureth net project The database into which data are being e
15. SH terms are placed into the bibliographic record could be important Terms in the right list are numbered and their order could be changed by pressing the buttons up and down Figure 12 illustrates the order of MeSH terms that was changed compared to the situation on Figure 10 ltranspl search 1 Ethics Committees Clinical A 2 Hematopoietic Stem Cell Transplantation 3 Codes of Ethics 4 Bone Marrow Transplantation ful un select heading Figure 12 The descriptor Codes of Ethics was transferred from the first to the third place by selecting it and pressing down twice Thesaurus TELS Thesaurus Ethics in the Life Sciences is a part of the data entry application and the user is able to select terms and include them into the bibliographic record Please find information about the TELS development at http www drze de BELIT thesaurus einfuehrung html la en The form for entering the TELS terms consists of a query field two selection lists and a number of buttons as is shown in Figure 13 The user selects the terms that are describing the document s content in the left list and place them to the right list using the gt button It would be very un practical and time consuming to transfer the whole TELS to the user s PC each time s he opens this form To limit the amount of data transferred the user first enters a string that s he thinks is included in TELS term s that describe the particular aspect of a
16. ancel More Info Cx g this type of fle a From https f unimed mF uni lj si Open it with the default application Perl b al c Figure 22 A dialogue window enabling the user to download XML ised records or open them in a XML viewer a Internet Explorer b Netscape c Mozilla Firefox Mandatory fields 20 creator creator date document number authors In the Documentary standards some fields are marked as mandatory they must be filled in every record As a rule mandatory fields are general They are not specific for any primary document type and are present in every data entry form These fields are creator creator date document number in national db author original title English title year of publication document type language thesaurus keywords In the data entry application the creator and creator date fields are entered automatically Creator is an institution that contributes the records and the field s value the institution s acronym is determined by the use of username Creator date is the date of the record s creation Creator is an important field because permissions for editing and deleting records are linked to it Document number in the national database 1s a number that is unique inside the subset of records contributed by each creator It is created automatically irrespective of the way the record entered the NMS data
17. andatory field but the data entry application doesn t check the presence of the field in the main form This is so because the English title is not necessary document s original element It could be made by an additional translation of the original title and it is quite natural that data entry and title translation is done by different people or and at different time This separation of task would not be possible with as strict checking as it is with the original title However it will not be possible to transfer the record into the final database without the English title Year of publication is a mandatory field and the user is forced to enter it prior to sending the main form to the server The application also checks if the value is integer number not longer than 4 digits and doesn t allow the user to send the form if this is not the case There are two kinds of document types primary document type and secondary document type The former is mandatory the latter which could have multiple occurrences is not Euroethics and Endebit treat this field slightly different Endebit allows that the primary and secondary type names are actually entered into separate fields The same way was chosen for the data entry application because it is always easier to concatenate than to divide fields if needed The primary document type is determined at the beginning of a record creation It is a fundamental attribute of the record and cannot be c
18. base the record was entered manually or sent as a download from the national database s via converting between formats The user doesn t have the possibility of changing this number Actually there are three different document numbers in a lifetime of a bibliographic record ina NMS database document number identification number unique number that the record will get in a final database and has nothing to do with data entry application and an identification number that the record gets in a NMS database The latter is the record s unique identification while it is maintained in the NMS database and is not exported into the final database Author is a multi occurrence group of fields that is entered in a special web form original title english title year of publication document type language thesaurus keywords that is not part of any document type determined main form Every document and database record about that document must have an author however this could be an anonymous or corporate author In Documentary standards separate fields are envisioned to accommodate authors editors and corporate authors but for the sake of simplicity the same data entry form is used here for all and using the drop down list marks the author s type Original title is a mandatory field and the data entry application doesn t allow the user to send the main form to the server without some data in this field English title is a m
19. cini 201 Series Pobicaion place po SS Publisher Slovensko zdru enje za urgentno medicino Pages 285 95 ISBN Document language T bul F cze dan dut eng I fin I fre I ger I hun I ita I iit I nor pol slo T lv I spa C swe Our aim was to assess the prevalence of patients with mental disorders MD who sought Abstract help in the Emergency service E5 during the period of Jan 1 March 31 2000 All physicians affiliated with the ES in Ljubljana Slovenia were interviewed The Order address submit reset close f Done unimed mF uni lj si Figure 3 Screen form of the document type analytic with some data filled in Not all text fields are equal in form and treatment Some are very long i e abstract some of medium size i e titles and some short i e 4 chars in the case of publication year Some textual fields are numeric in nature i e publication year collation and are converted as such prior to entering the database Into some fields structured data have to be entered dates have to be in a dd mm yyyy format e mail addresses and URLs have their own rules to obey Several field names in the form s left column are marked with asterisks These are mandatory fields that must be entered Without values in these fields the web form could not be submitted There is an extensive help files system accessible from each data entry form Each
20. clude the USE string Terms 1 and 5 in the right list of Figure 14 are such synonyms and will be automatically translated into their 13 mark TELS terms as important delete TELS terms set the order of TELS terms 14 preferred forms descriptors after the form will be submitted By pressing the button submit the list of terms that was compiled using this data entry form is transferred to the server and saved into the database The form is closed by pressing the close button This data entry application provides no real orientation in the TELS thesaurus It is of course much easyer to search and select the appropriate descriptors if one uses a proper thesaurus browser Our advice is to open additional web browser window and load TELS browser located at DRZE http www drze de BELIT thesaurus index_html la en The link Thesaurus Online Version brings you to the browsable hierarchical representation of the thesaurus It is not possible to transfer descriptors from TELS browser into the data entry application If the selected TELS term represents the subject that is particularly important for the current document the user checks the major heading check box and the term which is transferred to the right list after this receives the mark If a term was transferred to the right list by mistake the user should select it and delete by pressing the lt button below the right list The same action is needed i
21. connection and programs and other data thesauri cannot be stored on the user s workstation Every byte of data must be sent to the user each time it is needed The greatest challenge of application development becomes the minimisation of data transfer with maximisation of application power There is another complication inherent to data produced by NMS partners character sets All partners with the exception of Bulgarian partner are using Latin scripts but enriched with numerous special characters There is no standard character set belonging to the ISO 8859 family that encompass all these characters leaving us with only one possibility the UNICODE The application runs on the Linux workstation with Apache Web server Database is hosted with the MySQL DBMS Server side processing data entry forms generation and export formatting is done by Perl scripts while the JavaScript scripts are used for the browser side processing Converters are written in Java Most of the programming was done by Brane Lesko ek PhD database structures planning programming of converters output formats and this manual were done by Jure Dimec PhD both from IBMI How to enter record After entering username and password the first window with Eureth net logo and pointers to project s important addresses appears part of it is shown in Figure 1 This window will remain open during the use of the application There are four buttons in this windo
22. cs endebit Selecting euroethics will find all records belonging to this database as well as those that belong to both databases Selecting euroethics endebit will find only those records that belong to both databases the opposite is all databases In the previous versions of the data entry application only single number in the document ID field was allowed 16 primary type institution search string missing fields user jure document ID database all databases Elie rim E pias we euroethics institution endebit euroethics endebit search string Figure 19 Limiting the subset of records using the database name Possible values of a database search field can be seen Database name as a search criterion could be combined with other criteria Using documents primary types as search criteria limits the database to the subset of the same document type Using institution name creator name as search criteria limits the database to the subset of documents that were created by the staff of the same project partner If the searcher also belongs to the same institution then the result of a search is a subset where all records are editable Eureth net searching user jure document ID 347 database all databases gt primary type all documents gt institution all institutions a BASSO Fondazione Leilo e Lisli Basso Rome Italy documents with CDEI Centre
23. cument the user checks the major heading check box and the term which is transferred to the right list after this receives the mark as in the Figure 11 and Figure 10 0 x Book chapter conference paper analytic creator jure IBMI creation date 09 10 2004 document ID 224 updated 16 09 2004 Search MeSH headings e search Alamethicin 1 Codes of Ethics Bioethical Issues 2 Ethics Committees ciinicet li Bioethics Codes of Ethics Ethical Analysis Ethical Relativism Ethical Review Ethical Theory Ethicists Ethics Ethics Committees Ethics Committees Clinical Ra Y major heading up down Ee select heading un select heading EA T a Figure 11 Selection of MeSH terms is done by copying terms from the left to the right column Two terms were selected while the checkbox major heading was checked 11 delete MeSH terms set the order of MeSH 12 terms enter terms from Thesaurus Ethics in the Life Sciences If a term was transferred to the right list by mistake the user should select it and delete by pressing the lt button below the right list The same action is needed if the term was marked as a major heading by mistake It is not possible to un mark the term in the right list The term should be deleted first the check box major heading should be un checked and the term transferred again As it was the case with authors and uncontrolled terms the order in which Me
24. d Ordinal position fields Each uncontrolled term s record that came from the database has a delete button associated By pressing it and confirming the decision all data about the particular term are immediately deleted from the database The form is recreated without the deleted record To delete values in fields of a new record that hasn t been submitted yet it is enough to press the reset button Thesaurus MeSH Medical Subject Headings National Library of Medicine U S is a part of the data entry application and the user is able to select terms and include them into the bibliographic record The form for entering the MeSH terms consists of a query field two selection lists and a number of buttons as is shown in Figure 9 The user selects the terms that are describing the document s content in the left list and place them to the right list using the gt button It would be very un practical and time consuming to transfer the whole MeSH to the user s PC each time s he opens this form To limit the amount of data transferred the user first enters a string that s he thinks is included in MeSH term s that describe the particular aspect of a document s subject This string has to be entered into the Search MeSH headings field and search button has to be pressed The Figure 9 shows results of a search with the string ethic Book chapter conference paper analytic Netscape iol x Book chapter conferenc
25. de Documentation et d Information en Ethique des Sciences de la Vie et de la Sant INSERM Paris France missing ETHOX The Ethox Centre for Ethics and Communication in Health Care Practice Oxford United Kingdom search string FCCS Instituto de Bioetica Fundaci n de Ciencias de la Salud Madrid Spain rr J IDEM Informations und Dokumentationsstelle Ethik in der Medizin Goettingen Germany 1 hits items 1 1 _fi KIB Karolinska Institutets Universitetsbibliotek Karolinska Institutet Stockholm Sweden UMCN Universitair Medisch Centrum St Radboud Nijmegen Niimeqen The Netherlands 347 IBMI Institute for Biomedical Informatics Faculty of Medicine Ljubljana Slovenia NMEC RS book cha CERISS Center for Education Research and Information on Science and Society Milan Italy EIU Ethics Institute Utrecht Ethiek Instituut Utrecht Utrecht The Netherlands INRA ESR National Institute for Agricultural Research Paris France IZEV Interdepartmental Center for Ethics in Sciences and Humanities Tuebingen Germany UCB University Centre for Bioethics Brno Czech Republic euroethics CECIB Study Centre for Human Ecology and Bioethics Cardinal Stefan Wyszynski University IMEBF Institute of Medical Ethics and Bioethics Foundation LBC Lithuanian Bioethics Committee DIIUP Medical University of Sofia Department of International Integration and University Policy HSB National Medical Center Hungarian Society of Bioethics Delooz HH Eti
26. e paper analytic creator jure IBMI creation date 09 10 2004 document ID 224 updated 16 09 2004 Search MeSH headings ethic search Alamethicin Bioethical Issues Bioethics Codes of Ethics Ethical Analysis Ethical Relativism Ethical Review Ethical Theory Ethicists Ethics Ethics Committees Ethics Committees Clinical T major heading gt select heading un select heading submit close Figure 9 Data entry form for MeSH descriptors User limited the thesaurus to terms that include the string ethic The subset of MeSH that includes this string was transferred with the form and placed inside the left selection list The user is free to select and transfer to the right list as many MeSH terms as needed To complete the description of the document s subject several repetitions of the searching through MeSH and selecting in the left selection list will probably be needed The Figure 10 shows the MeSH entry form with four descriptors in the right list Two of them were selected from the MeSH subset made by searching with ethic and two after searching with transpl mark MeSH terms as important 0 x Book chapter conference paper analytic creator jure IBMI creation date 09 10 2004 document ID 224 updated 16 09 2004 Search MeSH headings trans search Bone Marrow Transplantation 1 Codes of Ethics Bone Transplantation 2 Ethics Committees Clinical Brain Tissue
27. er to enter these data for each or any author The order in which authors names are presented in a bibliographic record of a multi authored document is important To ensure that the authors positions will be preserved this information has to be entered to the field Ordinal position of author The 1 author should have number 1 entered into the field Ordinal position the 2 one number 2 etc If by mistake the authors were not entered in the correct order it is enough to change the numbers in their ordinal position fields The correct order of authors data will be restored after the form is submitted The Documentary standards include three fields denoting authorship namely Author Editor and Corporate author In order to simplify data entry the same form is used for all three fields An additional field Author s type is introduced to the form having values author editor and corporate author see Figure 7 The user should enter the name of the authoring entity into the Author field and describe whether it is author editor or corporate author in the Author s type field submit author data delete author data 3 Book chapter conference paper analytic Microsoft Internet Explorer Book chapter conference paper analytic creator jure IBMI creation date 09 10 2004 document ID 224 updated 13 10 2004 Authe DernovSek MZ Author s type aunor Author s affiliation thor jubljana Author s email ere edi
28. f the term was marked as a major heading by mistake It 1s not possible to un mark the term in the right list The term should be deleted first the check box major heading should be un checked and the term transferred again As it was the case with authors uncontrolled and MeSH terms the order in which TELS terms are placed into the bibliographic record could be important Terms in the right list are numbered and their order could be changed by pressing the buttons up and down Figure 15 illustrates the order of TELS terms that was changed compared to the situation on Figure 14 search 1 adult stem cells e tetal research Jembryonic stem cells 4 stem cells Fprimarcial stem cells b fetal development up down un select heading lt Figure 15 TELS terms from Figure 14 were reordered The descriptor fetal research was transfered from the 5 to the 2 place by selecting it and pressing up three times edit existing record search for records To edit a record that was just saved pressing submit button in the main form was the user s last action is easy Under the note with the confirmation of a successful saving of data there is a row of buttons as in a Figure 6 that enables the user to bring back the main form the author s form or any form with the subject description Each form is transferred from the server to the user s PC with data that were entered for that record in previous session s
29. g belong to the same creator institution Eureth net searching user jure document ID 34700 database all databases gt primary type all documents institution NMEC RS National Medical Ethics Commitee Republic of Slovenia 20 N search string P aramona I english title authors uterms thes MeSH go close missing 1 hits items 1 41 first lt lt revious lt gt next gt gt last bibliographic full record XML p grap 347 NMEC RS book chapter or conference paper Delooz HH Eti na vpra anja pri ivljenjsko ogro enih bolnikih kriteriji za zdravljenje Ethical issues in critical care criteria for treatment in Bru an A Gri ar M editors Urgentna medicina Izbrana poglavja 2 Zbornik 3 mednarodni simpozij o urgentni medicini 1996 jun 26 29 Portoroz Ljubljana Slovensko zdru enje za urgentno medicino 1996 147 564 euroethics main authors uncontrolled terms Thes Ethics Life Sci MeSH delete all data full record Figure 18 Record with ID 347 was found and is ready for editing It is possible to enter document ID as an interval of numbers in the form number hyphen number e g 500 800 leading to a longer list of search hits Blank spaces around hyphen are optional database This is one of the search fields that can be used for making a subset of records Possible values for a field are all databases euroethics endebit and euroethi
30. hanged after the record 1s created If the wrong primary document type was selected the record must be deleted and re created with the correct one The names of languages are three letters long and are conformant to the ISO 639 standard The field of check boxes is used for entering the language codes and more than one language code could be entered The field is mandatory designed to contain keywords and key phrases descriptors from the Thesaurus Ethics in the Life Sciences however presently there is no thesaurus incorporated into the data entry application The field allows multiple occurrences of keyword records There are several possible ways in which the thesaurus keywords will be linked to records Endebit partners will most probably use Endebit s Thesaurus tool or some off line method referencing the document number It is possible to incorporate thesaurus into the data entry application in the same way as MeSH headings are incorporated 21 Multiple occurrence fields Data entry forms 22 analytic chapter in a monograph conference paper Multiple occurrence fields or repeating fields are fields that can be present in the record in more than one occurrence Occurrences could be simple values such fields are secondary document type ISBN ISSN language or could be complex Such fields are author thesaurus keywords uncontrolled terms MeSH terms The secondary document type and language fie
31. independent carriers of information but are at the same time parts of bigger parent documents Examples of such documents are chapters in a monograph when they have different authors or papers in a conference proceedings To enable the end user to find an analytic document some basic data about the parent document have to be entered 1 e editor s names book title publisher s name and place in a case of a chapter in a book For an example look at this obviously fake bibliographic record in which underlined data describe the parent document and not the document about which we are primarily entering data Author A Author B Chapter title in a monograph about some very important Stuff In Editor A Editor B editors A monograph about some very important Stuff SomePlace SomePublisher 2004 12 34 This is a Somewhat complex situation in which data about two documents have to be entered into the same form s therefore special care have to be taken The Figure 23 shows part of the main data entry form for this record audiovisual material Original title Chapter ttle ina monograph about some very important stuff Book title lA monograph about some very important stuff Series SomePlace Publisher SomePublisher 2004 Pages f 2 34 Figure 23 A part of a data entry form of the primary type Book chapter conference paper analytic Data about chapter title and book title were entered Publicatic
32. lds are entered by checking check boxes multiple 1f needed Multiple ISBN and ISSN codes are entered into simple text fields but separated with semicolon signs Complex multiple occurring fields are actually multiple occurring records For each author for instance several data items could be entered family name and initial s of personal name author s role in a document author s affiliation e address and the record s ordinal position if there is more than one author Similarly the subject description terms could have accompanying data e g importance indicator or ordinal position Working with multiple occurring records is described separately Documentary standards describe the full document structure however it would be very impractical to send the data entry form with all fields and probably data in it to and from the user each time the communication event happens Moreover it is unnecessary Not all fields are possible for each document type therefore fields from the full structure are distributed into seven data entry forms one for each primary document type Some fields especially mandatory ones are present in every form i e titles language some are characteristic only for some document type i e ISBN ISSN and are present only in a corresponding data entry form Following are the descriptions of data entry forms and short instructions for their use This data entry form is prepared for documents that are
33. lection of records that aren t complete in order to fill missing values before transferring them to the final database The search hits are normally presented with editing buttons drop down list of database names and horizontal lines in between Such presentation is not very convenient for any other use except editing Certainly there are situations in which cleaner and more terse presentation is needed be it for planning of future editing work overview of one s contribution to the common database or compilation of the institutional backup For such purposes three additional buttons were added to the top of each search hits list These buttons are bibliographic full record and XML All three buttons trigger uninterrupted presentations of search hits lists without the previous and next buttons All the records corresponding to the values in the search request form are presented It is possible then to compose a list of all records in the database if all search form fields have no values entered An exception to this rule is a list made by the XML button bibliographic button opens a new browser window and fills it with a simple list of Medline style bibliographic records All records corresponding to the search request are presented regardless of the institution that entered them It is possible to print the list by using the web browser s printing functionality full record button opens a new browser window with a lis
34. na vpr A Gri ar M editors U Slovensko zdru enje NMEC RS National Medical Ethics Commitee Republic of Slovenia Figure 20 Limiting the subset of records using the creator s institution name Part of a list of possible values can be seen The programs check the records for the presence of the string of characters or numbers that is entered into this search field All textual fields are checked including the author and subject description fields The searching is not case sensitive This is the only field that is designed for real searching and not just selecting as the four fields standing above on a form The check boxes named english title authors uterms meaning uncontrolled terms thes meaning terms from Thesaurus in Life sciences and MeSH enable the user to select only records that doesn t have anything entered into these fields The option is very practical because it makes the separation of tasks during the data entry much easier One person may enter the basic data about the documents while 17 18 print or download records bibliographic button full record button XML button another person may index the documents or translates the titles at some other time With the thes or english title check box checked it is easy to select only those records that need indexing with TELS or translation of original title Another use of the check boxes is in se
35. ntered by this application is serving as an intermediary storage before the bibliographic records are transferred to the final Eureth net database s In this intermediary database bibliographic records contributed by partners from NMS countries are being collected They are mostly entered online In some cases local bibliographic collections exist and data from them are downloaded sent to the Institute for Biomedical Informatics IBMI where they are converted and uploaded to the database The idea behind the development of this application and intermediary database was that by using this approach it would be much easier to ensure the conformity to common documentary standards compared to any other possibility The data entry application is using WWW infrastructure for communication with users There are good and not so good consequences of that decision By not using the common client server approach the potential problems with software installation and hardware OS compatibility are avoided The user needs no special software to use the application and nothing more powerful than moderately capable PC with Internet connection and Web browser All the algorithms needed to collect and check data are part of Web pages and data are interchanged between user s browser and server s programs by using the simple HTTPS requests On the other hand relying on the Web infrastructure brings some clumsiness compared to client server systems There is no permanent
36. of a hits list the person that submitted the record 862 and the person that performed searching came from the same institution creator but this is not the case with records 863 and 864 Among search hits some have buttons that call data entry forms and some have not 15 as on Figure 17 The right to edit a record has only a person from the same institution creator that contributed the record and only bibliographic entries of such records have buttons that allow editing All fields in the search form are equal and connected with the operator AND when search is performed If fields database and institution are filled with values euroethics and IBMI the hits set will be an intersection of both i e containing only records made by IBMI and destined for the Euroethics database document ID This is arecord s unique identifier in the application s database Using it as a single value one number in the search request always brings at most one record If we compose a search request with the value 347 in the document ID field and value NMEC RS in the institution field the document 347 will not be found if it was created in some other institution or there is no record with this ID in the NMS database Figure 18 shows results of a search with document ID as a query The record found is ready for editing buttons that bring web forms with data are visible meaning that record s creator and a person that performed searchin
37. ong the fields that should be considered for data entry typically are the original and English titles for the paper s title book title for the proceedings title pages for the paper s pages e g 15 27 publication place publisher and ISBN for the proceedings data Conference paper s data and its parent s proceedings data are mixed on the same data entry form and that calls for a special care Data entry into the authors form is performed in the same way as it is described for the analytic document type and illustrated with Figure 24 journal article An article ina periodical other than newspaper with the ISSN An important but simple document type in terms of data entry newspaper An article in a general interest newspaper A simple document type in terms of data article entry grey literature Made for entities that have all attributes of real documents except that they are not published in a way that enables widespread access monograph A book with the ISBN An important but simple document type in terms of data entry Please note that the field Book title under the form s subtitle Article or chapter is reserved for the title of a book or conference proceedings when the document is analytic chapter in a book or conference paper For a monograph the title have to be entered into the Original and English title fields 24
38. t of records corresponding to the search request The list could be quite long because all data that were entered for each record are presented marked with standard short field names It is possible to print the list by using the web browser s printing functionality The purpose of the XML button is downloading of records The button triggers the composing of a file with records marked with XML style tags One of such records is presented on a Figure 21 Two criteria are used for selection of records the values in the search request fields and ownership of records Of search hits only those that were entered by the users from the institution of the person performing download are included into this file The file has an automatically constructed filename composed of the user s username and a string _records xml By downloading the records in XML form the institution that entered them could maintain its own backup copy XML format of records is standard and self describing and thus the records are easy to be included in some future database with differing structure Instead of presenting records in a new window the data entry application opens a dialogue window which offers a possibility to save records to the user s PC or view them with a XML viewer These dialogue windows slightly differ with different web browsers used Figure 22 shows dialogue windows of three most popular web browsers a Internet Explorer b Netscape and c
39. tor h Ordinal position of author Author s type C Author s affiliatior Psihiatri na klinika Ljubljana i Author s email Irdinal position of author Author s type editor gt Author s affiliation Author s email Urdinal positior of author Author Author s affiliatior a Authorsemal De be ee Ordinal position of author Figure 7 Data entry form for authority information Three different types of author s roles are shown Each time the authors data entry form is called be it for the first or n time or during the data editing there is place for one new author on the form When data about this author is entered pressing the submit button sends it to the server and the form is returned with the place for one more author This data entering cycle could be repeated as many times as needed To interrupt it press the close button The application tests the value entered into the Author s e mail field It must obey a general form of an e mail address For each author the Author name Author s type and Ordinal position fields must be entered With any of these fields empty the form can not be submitted Author affiliation and Email fields are optional Each author s record that came from the database has a delete button associated By pressing it and confirming the decision all data about the particular author are immediately deleted from the database The form is recreated without the deleted
40. w the left pair leading to the data entry and search and edit lines of work Pressing the right pair of buttons brings this manual and dynamically created overview of database contents with simple statistical data respectivelly The value for a creator field and the user s name are also displayed Bibliographic data entry for Euiroethics and Endebit databases creator IB hil user jure Data entry ser manual ve search and Edit otatistics Figure 1 Part of the application s first window By pressing the Data entry button the working window opens All the data entry searching and editing forms will be presented in this window Eureth net data entry Netscape iol x Eureth net data entry user jure database chooseone v primary document type choose one new record close euroethics endebit euroethics endebit Figure 2 Beginning of the data entry work determining the database and primary document type Data entry starts with selecting from two selection lists in order to determine the most general attributes of a future record the database into which the record will go and the primary document type Regarding the database there are three possibilities to choose from each of the Eureth net databases and both and seven primary document types New record button will bring the appropriate data entry form but only if database and primary type have been selected Button
41. with XML files In case of Netscape or Firefox the viewer must first be selected A good choice of such programme is a reasonably new version of any web browser To select it first check Open it with b or Open with c and use drop down list to browse to a programme of choice Their positions could differ on different PCs but standard installations are Program Files Netscape Netscape Netscp exe for Netscape and Program Files Mozilla Firefox firefox exe for Firefox 19 File Download i x Opening jure_records xml x Opening jure_records xml xj C Ree The file jure_records xml is of type text xml Extensible Markup Language h h Some files can harm your computer If the file information below and Netscape does not know how to handle this file type This file s located You have chosen to open looks suspicious or you do not fully trust the source do not open or at s d save this file https unimed mF uni lj sifetika pee aE File name jure_records xml What should Netscape do with this File which is a XML Document File type XML Document From arenes open tt wth r What should Firefox do with this file 5 mafur pen it wi Save it to disk Open with firefox exe O Always show this dialog before handling files of this type ie Save to Disk Would you like to open the file or save it to your computer za _Cancel_ l Do this automatically For files like this From mow on Open i i C
42. x Journal article creator jure IBMI creation date 21 03 2005 document ID 1637 updated 15 12 2004 development fetal USE fetal development 1 somatic stem cells USE adult stem cells donation fetal tissue USE fetal tissue donation 2 embryonic stem cells fetal blood USE cord blood 3 stem cells fetal death USE stillbirth 4 primordial stem cells fetal development 5 fetal experimentation USE fetal research fetal diseases USE fetal therapy 6 fetal development fetal experimentation USE fetal research fetal medicine fetal reduction selective USE selective abortion fetal research fetal stem cells fetal therapy x I major heading up down select heading un select heading lt Using data from Thesaurus Ethics in Life Sciences version 2004 Use regulated by the Licence Agreement Done unimed mf uni lj si VW Figure 14 Four TELS terms were selected after searching with cells and two after second searching with fetal Terms 1 and 5 are synonyms of preferred terms and will be translated to them after submition of form The Figure 14 shows the TELS entry form with six descriptors in the right list Four of them were selected from the TELS subset made by searching with cells and two after searching with fetal Searching through TELS results in the subset of descriptors and synonyms that include the searched string Synonyms could be recognized because they in
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