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3. fields red and allowing you to press the Harvesting button Publication Harvester and Colleague Genera Software Reouiements Specification lipase ua aren ne reran oes verntaa 1f the harvest is interrupted due to a system crash or shutdown the software will treat it as if the harvest Were interrupted properly In this case again push the Clear Errors and Resume Previous Harvesting step When the Publication Harvester loads a database it immediately checks for interrupted data If any interrupted data is found then it displays those errors turning the labels red to alert you that there s interrupted data or errors and enables the Clear Errors and Resume Previous Harvesting button This check can take a long time up to a few minutes on very large databases You can turn off this check by unchecking the Check for interrupted data checkbox Warning Unchecking the Check for interrupted data checkbox can lead to unstable databases Only use it if you are absolutely sure that the Publication Harvester software completed its last run on the database This checkbox is very useful for quickly opening up a database so that you can generate reports but it should not he used until all ofthe people in the database are completely harvested 3 3 Retrieve Publications in Other Languages By default the Publication Harvester will only retrieve publications that are in English using the Languages field i
4. To open this log in Notepad and save a copy of its contents to disk click the Open in Notepad button ere faerie eee ani e Fer Ta fo Ghost ober 2 or 6 Setting publications For tablan A34015329 number 3 of 6 10 27 2008 12 2 oea i ier i 3 10 37 2008 12 1f there are errors for example if the local network goes down preventing the Publication Harvester from contacting the NCBI server to issue PubMed queries then those errors will appear in the log The people will be tagged in the database with errors so that you can retry those people later using the Clear Errors and Resume Harvesting button see below Some Medline queries will not retrieve any publications when this happens a warning will appear in the log 1f there are many rows in the People file the harvester could take a long time to retrieve and process all of the publications To make it easier to deal with large data it is possible to interrupt and continue the harvesting operation To do this lick the Interrupt Current Harvest button You may also click the X button in the upper right hand corner of the window to close the window if you do this while harvesting publications the software will prompt to verify that you really want to interrupt the harvest the People with Errors and or ear Errors and Resume 1f the harvest is interrupted the software will indicate this by color the People Not Harvested
5. click the button next to that field it will pop up the ODBC Data Source Administrator Click on the button next to the People file field and browse to the People file see section 3 1 1 Then click on the button next to the Publication type file and browse to the Publication Type Categories file see section 3 1 2 Once these forms are filled in the Publication Harvester window will look like this 1 Publication Harvester and Colleague Genera Sofware wlrements Specification o TE pee mena norte aona neresen rae ne agrees en an me aa Hoeser o A PubMed server and begin retrieving publications pee mena nurten aung meresan arse an egret en a me Hoes ranman ai a E To begin harvesting data click the Harvest Publications button The software will connect to the The software will run until it completes this harvesting step Note that for very large databases with over 50 000 people performance may slow down due to the fact that it takes time to update the 2 Publication Harvester and Colleague Generator Software Reoulrements Specification statisties in the Database Status box Uncheck the Update these status numbers during harvest box to prevent this The box will not significantly speed anything up for small databases As it retrieves publications it adds entries to the log at the bottom of the main window
6. information in the specified file Any publications with any of these people will be disassociated with them They will not be removed from the database however since they may also be associated with other people To remove people click the Remove People button The software will prompt you for an Excel file containing the people to remove Any of these people who are in the database will be removed Any people who are in the file but not the database will be ignored 3 5 Generate Reports To generate the reports based on the harvested publications click the Generate Harvesting Reports button The following window will pop up pees ee napon us Bewe 7 o A Birman pirea H 1 auena etry paesane aaa Gaia on lus nang n peta eer vme Ta a eer st engine cme Pests The system will generate up to four different reports the people report the publications report the MeSH headings report and the Grant IDs report By default all four will be generated indicate that certain reports should not be generated by unchecking them in the Generate Harvesting Reports window The People and Publications reports have fault tolerance built in The report generation process is very time consuming and if it is accidentally interrupted the software will give the user the option to either overwrite the reports or continue where the previous reporting ended The reports will be written to the z
7. is to serve as a guide to people who want to use the Publication Harvester software It should give them all of the information necessary to install configure and use the software 1 2 Scope This document contains step by step instructions to show users how to install configure and use the Publication Harvester software on a machine running Windows XP It covers Downloading and installing the NET Framework 2 0 Downloading and installing MySQL 5 0 Downloading and configuring MySQL Connector ODBC Creating a new MySQL database Creating an ODBC data source Installing the Publication Harvester software Preparing the input files Using the Publication Harvester to retrieve publications from PubMed Using the Publication Harvester to generate reports 1 3 System Overview The purpose ofthe Publication Harvester is to generate an accurate count of publications for a set of people using a set of possible name variations for that individual and recording author position carefully Publication Harvester and Colleozue Generator Software Reguirements Speciation 2 Installation This section describes how to install the Publication Harvester software It covers Downloading and installing the NET Framework 2 0 Downloading and installing MySQL 5 0 Downloading and configuring MySQL Connector ODBC Creating a new MySQL database Creating an ODBC data source Installing the Publication Harvester softwa
8. Publication Harvester User Manual v1 0 23 2008 Steliman and Greene Consulting LLC p ivwvstlinan sreenecam Perms ix grat cap dtr andlor mois is document der the terms of he GNU Fr Documentation License Versi 2 arany ltr verso published by the Froe Sota Foundation with no avant Sectans no Frant Corer Tet and wo Back Cover ent copy af the lense include in tbe ecto eed GNU Fro Documentation ices Publication Harvester and Colleague Generator Software Reouiements Specification Table of Contents 1 Introduction LE Purpose 12 Scope 13 Sistem Overtow 2 Installation 21 Download and Install the NET Framework 20 22 Download and Install MYSQL 5 0 24 Download and configure MySQL Connector ODBC 24 Create a new MYSQL database 25 Create an ODBC Data Source 26 Install the Publication Harvester 3 Prepare the Input Files 3 1 People File 3 12 Publication Type Categories Fi 22 Retrieve Publications from PubMed 33 Retrieve Publications in Other Languages 424 Maintain the List of People 35 Generate Reports 351 People Report 352 Publications Report 353 MeSH Headings Report 3S4 Grams Report 4 Importing Data into Microsoft Access 2003 5 GNU Free Documentation License 6 Revision History n n 6 Is is 18 19 2 z z Ei as 20 3 Publication Harvester and Colleague Generator Sofware Requirements Specification 1 Introduction 1 1 Purpose The purpose ofthis document
9. Tonal mi of pals in year Bins TIT AE TME 2 war wahid _123pubeouni pos Weighted wat nb of pubs in year bias LT M T eno ype NOY T Taea Toil a of pubs in year BaT wahid_Ipabeouat Weighed otal nb of pubs in year Bin T Tpubeount_ por Total a of pubs in year bin Tibor Twahid_Ipubeouat post Weighted toa nb of pubs in year Bin T aur Publication Harvester and Colleague Generator Software Requirements Specification TN Number J Toatab of pubs in year Din T Tast ankor wahid Tpubeouni pow Number Weighted total nb of pubs in year Bin T Tst makor Tpubsount post Number Total nb of pubs in year bin 1 middie author wahid Tpubcouni post Number Weighted total nb of pubs in year bin T middie muior Tpubedunt pos NTI Number Total nb of pubs in year bin nextlast aor Twghid_Ipubeouat posNT Number Weighted total ab of pubs in year bin T nex aia Tpubeount pos Number Toral ab of pubs in year bin T author wahid Ipubeount po Number Weighted total nb of pubs in year bin T author Pabiieaton ype category 2 E Number J Toal nb of pubs in year Bin TT Tah pubeouat Number Weighted total nb of pubs nye Spubeount_posl Number Total ab of pubs in year bin 11 T7 wahid Ipubeouni posl Number Weighted total nb of pubs in year bin T auta Zpen pos Number Toral nb of pubs in year bi
10. a Tast auto Wahid 2pubeoual pow Number Weighted total nb of pubs in year bin st autor Spubeount post Number Total nb of pubs in year bin I middie author Tghid_ 2pubeouat PONT Number Weighted total nb of pubs in yea Bin TI middie author Spubeount_posNTL Number Total nb of pubs in year bin T next to last author wahid Ipubeount pooR TE Number Weighted total nb of pubs in yea bin TI netto tast aur Ipucu pas Number Toral nb of pubs in year bin TE author wam 2pubeount po Number Weighted otal nb of pubs in year bin 11 anor Publication pe category T E Number J Toral nb of pubs in year Bin TIT wami pubeount Number Weighted total nb of pubs in year Bin TT pubeount_ por Number Toral ab of pubs in yar bia T author waht 3pubeouni posl Number Weighted total nb of pubs in year bin TIT Tahar pubcount_ pos Number Total nb of pubs in year bin st author Twahtd_Spubcouat ON Number Weighted total nb of pubs in year bin lat anor pubeount_ pos Number Total nb of pubs in year bin TT middie autor wami 3pubcount post Number Weighted total nb of pubs in year bin I middie mhor Spubeount pos NTI Number Tota nb of pubs in year bin HT next to last author wahid 3pubeount posNTE Number Weighted total nb of pubs in year bin TIT next io ast aio pubsount pos Number Total nb of pubs in y
11. al PubMed formatted name named text optional PubMed formatted name medline_searchl text A search term which will be used to execute the PubMed search For example van eys j au OR var s j au OR eys 4 tau Mlau OR tobi je aul OR tobian 13 au reemtsma Kk au OR reemtsma kb au AND 1956 2000 ap1 guiilenin re au OR guillemin r au NOT Electrodiagn Ther ta OR Phys Rev Lett ta OR vegas ad OR lindle au A sample people file can be downloaded from the following URL hhup www stellman greene convPublicationHlarvester sample input xls Note In addition 10 an Excel file the People file may also be CSV format which is useful if you need to harvest publications for over 65 535 people the maximum size of an Excel file 3 1 2 Publication Type Categories File The Publication Type Categories file is used by the software to divide articles into categories based on publication type Each PubMed article has a publication type The software must either discard each n Publication Harvester and Colleague Generator Software Requirements Specification publication or populate the Publications PubTypeCategoryID column based on that publication type The PublicationTypeCategories esv is a comma delimited text file which the software uses to determine how to process the publication types Publication TypeCategories csv contains two columns PublicationType
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13. ar as queried I aukar pukenut post Toral nb of pubs in year as queried Tast autor akd pibeount posN Weighted toal nb of pubs in year as queried Tast author pubeount posht Total nb of pubs in year as queried middie author Wam pabeoun pos Weighted ita ab of pubs in year 23 queried middle har puien posh Toll ab of pubs in year as queried next io Tast author wahi pubcount pos NTE Weighted total nb of pubs in year as queried nex 10 a autho pubsount pox Total a of pubs in year ax queried author waht pubcount po Weighted toal nb of pubs in year as queried Pme I publication type categories 1 and Trpo Toul ab of pubs in year bins LIT TT a Tps Weighted ttl nb of pubs in year bins TIT ETIT TESpubcount_posl otal nb of pubs in year Bins LIL MI author wahid T23pubeouni posl Weighted toal nb of pubs in year Bins TT 1 Tankar TESpubcount pos Total ab of pubs in year Bins TIT AE Tas author wahid 2ipubcount pot Weighted ial nb of pubs in year bins LIL amp I sar TESpueount_ pos Toul ab of pubs in year bins LITT middle nahor ain T2pubcount poa Weighted ttl nb of pubs in year bins LIT TIT middie mathor T23pubcount posNTL Tonal nb of pubs in year bins TAIT A I next iorast mthar wahid T23pubeount paN TT Weighted toul nb of pubs in year Bins TIT 1 nexo iet mor TESpubsount pon
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15. contains one row per person per year per MeSH heading T Description Senke E Person unique dentier Yeu key Number of publication Heading Text H Healing Count Namba Numer of MeSTT Reading fort penn We eT TE 3 5 4 Grants Report The Grants report contains one row per person per year per publication per grant ID sorted by year T Tyre Description Year Number Year of publication PMID Number Publistion 1D Gran Text Gran forthe publication re may be several ows pe PUBCON one per gant ID Publction Harvester and Colleague Genera Sofware Reguirements Specification 4 Importing Data into Microsoft Access 2003 Many researchers use Microsoft Access to manipulate data The MySQL Connector ODBC which is required by the Publication Harvester see section 2 3 allows Microsoft Access to easily import data from a Publication Harvester database To import Publication Harvester data into Microsoft Access 2003 first open the database that you would like to import data into Then select the File Get Extemal Data Import menu option Access will pop up a File Open dialog box At the bottom of the dialog box is a dropdown list labeled Files of type Select ODBC Databases from this list This will cause the following window to pop up tee Ah ae macte aan ct iner aas BE eenaa r mro nannaa ey Publication Harvester and Colleagu
16. d configure MySQL Connector ODBC The Publication Harvester uses a piece of software called the Connector ODBC To install this go to http www smysal com downloads and look for the link labeled Connector ODBC 3 51 Generally Available GA release the version number may be different Click on that link That page will have a section labeled Windows Downloads Find the row in that section labeled Driver Installer MSI and click on the Pick a mirror link Scroll down this page and click on any of the links labeled HTTP or FTP This will link to a file that ends with msi Save that file and double click on it The following window will pop up u Welcome to the Setup Wizard for MySQL Connector ODBC 3 51 sng wane nine pcan a Sian araneae tern oa Select Typical and click Next gt n Publication Harvester and Colleague Genera Sofware Reguirements Speciation ay te utat rope L kisal Click Install When the installation completes the following window will pop up Wizard Completed Click Finish The MySQL Connector ODBC is now installed 2 4 Create a new MySQL database The Publication Harvester requires that you create a MySQL database for it to use You will give this database a name It doesn t matter what name you give it In this example we ll use the name Publication Harvester To create the database first se
17. e Generator Software Renulements Specification Click on the Machine Data Source tab The data source that you created earlier see section 2 5 should appear in the list In this example the data source is called Publication Harvester Select that data source and click OK Access will then display the list of tables in the database Import Objects falesa iets asa cree meshheadings Cancel pene Peosepnicrtns Cem ubicatoneutnors a pubienbongrant Deselect Al lbubicatonmeshreacings pubicatons pubtypecategones starcolasguas Select any tables that you would like to import into Access and click OK Access will copy the data from MySQL into your Access database For more information on the structure and contents of the tables see the Publication Harvester software requirements specification Note that any other data management or analysis tool which uses ODBC data sources can import data in the same manner Publication Harvester and Colleague Generator Sofware Reguirements Spetietion 5 GNU Free Documentation License Tbe pupene ot dis an ek cia and aeit deme ent in en yt aar and sir a gett raw wc a ng ces repens o dikentot made Oar GNU Gena eit eh nasi emda far a sae edn di sink wt a oc ia satan pot cae Epen at is awh a i pilda asa ied eal We mon on cds evo wie eho hn Leen i ay mama ar oda wost ay ma hn i ye ap ing en be diamonds yoyo nr hc nin eg Foi nr yi be
18. ear bia 111 27 umor Tah 3pubeouni paT Number Weighted total nb of pubs in year Bin TI P maar Publication ype category T ipubcoumt Number J Total nb of pubs in year bin TV wahid _IpubcounT Number Weighted total nb of pubs in yea Bin TY puedan post Number Toral nb of pubs in year bin TV I author Twahtd_spubeouni posl Number Weighted total nb of pubs in year Bin TV T author Ipubsoun_posN Number Total ab of pubs in year bia TV Tast autor wahid Ipubeouni pow Number Weighted total nb of pubs in year Bin TV as aaar Ipubsount posh Number Total nb of pubs in year bin 1V middle author wahid _Ipubcount pT Number Weighted total nb of pubs in year Bin TY middie aukar pubsouat_ posN TI Number Tota nb of pubs in year bin TV next to last author Twghid_spubeount_poaNTL Number Weighted ttl nb of pubs in year bin IV nextlast aur puedan pos Number Total ab of pubs in year bin TV 2 anor Wahid pubeount po Number Weighted ota nb of pubs in year Bin TV 2 aor When a column is noted as queried that refers to all bins I I II IV and publications without a bin In each of the Pubcount columns the bin refers to the PublicationType value for the publication For example the 4pubcount_pos refers to any publication with a PubTypeCategorylD of 4 where the person is in the first author position PersonPublications PositionType 1 The Pubeount columns are
19. eatanapc wit Cl Doramas weet Fintan stirrer 9 one tary nar cet Cane pede tusirenage enero Bem paeen Some Ca Serta tai ite 7 Eimon miannan onenen z aamen Stig ceo meal ns AE eaa e a Dn In the above example the section 2 4 will be added to the report This will add a section with columns named 24pubcount wehtd_24pubcount ete These columns will contain the values for all publications with categories 2 or 4 Publication Harvester and Colleague Generator Sofware Requirements Specification 3 5 2 Publications Report The Publications report contains one row per publication based on data in the PersonPublications table Ta Type Description scab key Text Person unique eae pmid key Number Unique article identifier journal name Text Name of journal yea Number Year of publication Moni Text Month of publican Day Number Day of publication Tae Text ale le Volume Tex lume number of the Journal in which the article was published Tue Text Tsu in which The ates was published Position Number Position in authorship Ts abauthons Number Number of coauthors Gnelading The person Bin Number From Yo TV based onthe Pab Type ar Pager Text Page numbers m ageney Text Agency who awarded The grant Publication ype Text Publication Type from Medlin og a 3 5 3 MeSH Headings Report The MeSH Headings report
20. it Click Test to make sure the database works The following window should popup 4 5 econ mas ae Ce Click Ok The ODBC data source has now been created and should show up in this list 208 seen DSN i Or Fea Comeon Panina Atoe 2S Eo eee Click OK to close the window 2 6 Install the Publication Harvester The Publication Harvester installer can be downloaded from bttp www stellman greene com PublicationHarvester bin latest Download the ZIP file that contains the installer for the 16 Publication Harvester and Colleague Generator Software Reouiements Specification latest version extract it and run setup exe This will install the program into the start menu it will be listed under Publication Harvester In addition there are three sample files that can be downloaded from the Publication Harvester website to help you get started sample input xls sample input People file Sample JIFs xls sample JF file for generating reports Sumple pubiypes esv sample publication types file The Publication Harvester program will pop up as soon as the installer completes You can run it again at any time by selecting it from the Start menu Publication Harvester and Colleague Generator Software Requirements Specification 3 Using the Publication Harvester Now that the Publication Harvester has been installed it can be used to retrieve publications T
21. lect Run from the Windows Start menu n Software Requirements Svecficat Type create database PublicationFlarvester and press enter The database is now created Type exit and press enter to close the window 2 5 Create an ODBC Data Source The Publication Harvester connects to the MySQL database using a feature of Windows called Open Database Connectivity or ODBC ODBC allows you to store information about how to connect with a database Before you can run the Publication Harvester you must create an ODBC data source using the ODBC Data Source Administrator Publication Harvester and Colleague Genera Software Requirements Spectietion Select Run from the Windows Start menu oes Ce Ce Enter odbead32 and click OK The following window will pop up e m cot Scroll down to MySQL ODBC 3 51 Driver and click Finish The following window will pop up Is Publication Harvester and Colleague Generator Software Requirements Spectietion Mysa Connector ovac see opa va oe p Enter Publication Harvester as the data source name localhost as the server and anonymous as the password Click the own arrow at the right hand side of the database box to display the list of databases The PublicationHarvester database that you created in section 2 4 should be in the list in all lowercase Select
22. mutually exclusive so that within a bin the total pubcount is equal to the sum of the individual author pubcounts For example in any row the value in 3pubcount must equal 3pubcount_posl 3pubcount_posN 3pubcount_posM 3pubcount_pos2 Spubcount_posNTL Publication Harvester and Colleague Generator Sofware Reguirements Spetietion The Wehtd_Pubcount columns contain the count of publications for each journal for the year multiplied by the weight of the journal from the Journal Weights input table If a journal name cannot be matched in the Journal Weights file the corresponding publication is ignored in the weighted pub count ie itis assigned a weight of zero By default the People report contains two key columns setnb year and five sections based on the publication type category sum of all categories all sum of categories 1 through 3 1 2 3 category 1 category 2 category 3 and category 4 The report can be customized to add or remove sections To remove a section from the report click on it in the People Report Sections list and click Remove prere pp saae a O a rane piee 3 oram tary naar opt Cn ee ane sheng resron eee le a C e octyatoier ie 10 ener El poma wore In the above example the 1 2 3 section will be removed from the report To add a section to the report enter it in the Section to add box and click Add owmi
23. n the program Languages ist ot Medine language sbtrevistons separated by commas Hank tar no rastiin leo You can instruct the software to retrieve publications in different languages by changing the value in this box To make the Publication Harvester retrieve publications in Spanish English and Russian set the box to contain the following value Longueges ist of Medine lerguoge abreasons separated by comms en for no restor spacngras Publication Harvester and Colleague Generator Software Reguirements Specification The list of acceptable language abbreviations can be found at the MEDLINE PubMed Language Table web page http www nlm nih gov bsd language table himl The Languages box should contain a list of abbreviations separated by commas with no spaces To remove all language restrictions and harvest all publications regardless of language leave the box blank Longages it ef Medine language sbbrevistone separated by commas bank for rotation 3 4 Maintain the List of People You may change the contents of the database after it is generated by adding updating or removing people To add or update people click the Add Update People button The software will prompt you for an Excel file in the same format as the People file see above section 3 1 1 containing the people to add or update Any person in this file who is not in the database will be added any person who is already in the database will be updated with
24. o do this a set of input files must be prepared Then those input files can be used to tell the software whose Publications to retrieve and what to do with them Once the publications have been retrieved the software can generate reports 3 1 Prepare the Input Files The Publication Harvester uses two input files the people file which contains a list of people to retrieve and the publication type categories file which divides the publication types into a set of categories so articles can be classified by publication type 3 1 4 People File The People File contains a list of people and information which tells the software how to retrieve the data from PubMed for those people It is provided as a Microsoft Excel 8 0 file with the first row containing column headings The file contains the following columns setnb text The unique identifier for the person first text The person s first name middle text The person s middle name or initial may be blank last text The person s last name namel text The PubMed formatted name which will appear in the author list of a publication retumed by an NCBI query Only publications that have this name or the name in column name2 name3 or named will be added to the Publications table name2 text optional Another PubMed formatted name If more than one name is provided the software will look for publications which match any of the names name3 text option
25. o version 1 021 added multiple language support Andrew Steliman Updated to version 10 23 ded Check Tor Interrupted Dats chectbor and improved error handling and logging
26. or Sofware ulrements Specification et mso ever en att te dn WS SA TMa ata a When the installation is done the software will display this win E dow Click Skip Sign Up and select Next gt Publcation Harvester and Colleague Generator Software Reguirements Spectietion Wizard Completed eon ya Server now Sinister ines Sermo oeme tere ieee gt Sse lt e Publication Harvester and Colleague Genera Software Reguirements Spectietion Select Standard Configuration and click Next gt Bimota etom sere pria Biana enaa srar nanna fem encim ninao tane 22 Saris You must now enter a password for your MySQL server Enter the password in both text boxes and make sure that both the Modify Security Settings and Create An Anonymous Account checkboxes are checked Click Next gt Ormco cere ra ca a cain w Publication Harvester and Colleague Genera Software Reouiements Speciation Click Execute to configure the MySQL server MySQL Server Instance Configuration Wizard MYSQL Server Instance Configuration Configure the MySQL Server 5 0 server instance Proczsana contiaracen 1 eps conkasston vie ote Cre iS Seve Sm Sae a Press Finish to close the Wizard Click Finish MySQL 5 0 is now installed 2 3 Download an
27. re 2 1 Download and Install the NET Framework 2 0 The Publication Harvester requires the NET Framework 2 0 which can be downloaded from the Microsoft website Go to http www microsoft com downloads details aspx FamilyID 0856EACB 4362 4BOD 8EDD AABISCSE04F5 and click on Download to download the file dotnetfx exe Save this file to disk and double click on it The following window will pop up Click Next gt Check the checkbox and click Install gt The software will install automatically When the installation is complete the following window will pop up Pulblcaion Harvester and Colleague Genera Software Reouiements Specification Click Finish 2 2 Download and Install MySQL 5 0 The Publication Harvester software uses MySQL 5 0 to store its harvested data MySQL is a free and open source database The latest version can be found here hitp dev mysgl com downloads To download the latest version of MySQL 5 0 go to that page and follow the lnk labeled Generally Available GA release recommended Find the Download link labeled Windows Essentials 86 Download the file it will end with MSI and double click on it The following window pop up Welcome to the Setup Wizard for MySQL Click Next gt The following window will pop up This will begin the MySQL Server 5 0 installation Publication Harvester and Colleague Generat
28. string The publication type that appears in a PubMed article PubTypeCategory1D text This will typically be 1 2 3 4 or 0 This contains the numeric category or bin into which the software must classify the any article with the type specified in the Publicationype column If this column contains 0 the software ignores any publication with the type specified in the Publication ype column A publication may contain several publication types Normally the Publication Harvester only reads the first publication type However there are some publication types like Review that always occur as a second or third publication type To specify that this category should override the first type in a citation specify a negative publication type So if the category Review should be given bin 2 but should always override the first publication type then the publication types file should contain a value of for this category A sample people file can be downloaded from the following URL http www stellman greene com PublicationHarvester sample pubtypes csv 3 2 Retrieve Publications from PubMed To retrieve publications from PubMed first launch the Publication Harvester by double clicking on the PublicationHarvester program downloaded in the section 2 6 The main form of the Publication Harvester will pop up Click on the ODBC Data jource field and select the data source created in section 2 5 If you
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