SC/Gen and the Social Networking Report
Contents
1. Once you ve copied all of the publications click Step 3 Retrieve Colleague Publications This does exactly the same thing for the colleagues as the Publication Harvester does for the stars it downloads the publications from PubMed for each colleague Note If this process is interrupted or the machine is shut down you can restart the harvest later The SC Gen software will pick up where it left off without losing any data Once the colleagues are harvested it updates the Colleagues Harvested box which contains the number of unique colleagues that have had their publications downloaded and the Colleague Publications Downloaded box which contains the total number of unique publications if two colleagues coauthored the same publication it will only be counted once Publication Harvester and Colleague Generator Software Requirements Specification SC Gen Stars Colleague Generator ODBC Data Source Name Publication Harvester Roster File SS gt C Documents and Settings Andrew Desktop sample roster csv Database Status Tables Created People People Harvested Publications Found True 2 2 871 People With Errors People Not Harvested Colleagues With Errors lo 0 lo Step 1 Read the Roster file Roster Rows Step 2 Find the Potential Colleagues Stars with Colleagues Step 3 Copy Publications from Another Database Star Colleague Pairs Found Step 4 Retrieve2. this is the second degree social network 1 4 References The SC Gen software requires a database that was created using the Publication Harvester software This manual does not explain the use of that software the manual and specification of the Publication Harvester software can be found at http www stellman greene com PublicationHarvester This manual does not go into detail about what constitutes a colleague the formats of the input files and the reports or the structure of the database All of that information can be found in the software requirements specification SRS http stellman greene com SCGen SRS_Colleagues doc Publication Harvester and Colleague Generator Software Requirements Specification 2 Installation This section describes how to install the SC Gen software 2 1 Before you start SC Gen is built to operate on a database that was created by the Publication Harvester The SC Gen software also requires NET Framework 3 0 MySQL 5 0 and MySQL ODBC 3 51 You can find installation instructions for this in the manual for the Publication Harvester which can be downloaded from http stellman greene com PublicationHarvester Publication 20Harvester 20Manual doc 2 2 Install the SC Gen and Social Networking software Download the latest version of the SC Gen and Social Networking installers from http stellman greene com SCGen bin latest unzip it and run setup exe to install the software Once each i
3. 1985 Effie gt na P Jaa 1994 Alice Colleague ioe Constance 2000 gt 2005 2 degree star 2001 1995 2002 gt Roger 2nd degree star 2003 Justin ar 1996 1999 gt 2005 John 24 degree star This picture shows the social network for a colleague named Alice who is the colleague of two people on the original list Carol and Justin Those people appeared in the list that was fed into Publication Harvester and when their publications were downloaded Alice appeared on both of them She coauthored publications in 1991 and 1993 with Carol and in 1995 with Justin Mallory Joe Lisa Effie Roger and John also appeared on the list that was fed into Publication Harvester A second database contains the square data the colleague lists for each person restricted to only the people who were in the original list Since Alice is a colleague of Carol who is a colleague of Mallory then Mallory is a second degree colleague of Alice 4 3 Generating the social network report The goal of the report is to identify the way the relationship between Alice and Bob changes on a year by year basis To do this it contains a set of rows for each combination of colleague first degree star and second degree star In this example there are four combinations Alice Carol Bob Alice Eve Bob Alice Justin Bob Alice Mallory Bob Each of these four sets of rows will contain one r
4. License Any other attempt to copy modify sublicense or distribute the Document is void and will automatically terminate your rights under this License However parties who have received copies or rights from you under this License will not have their licenses terminated so long as such parties remain in full compliance 10 FUTURE REVISIONS OF THIS LICENSE The Free Software Foundation may publish new revised versions of the GNU Free Documentation License from time to time Such new versions will be similar in spirit to the present version but may differ in detail to address new problems or concerns See http www gnu org copyleft Each version of the License is given a distinguishing version number If the Document specifies that a particular numbered version of this License or any later version applies to it you have the option of following the terms and conditions either of that specified version or of any later version that has been published not as a draft by the Free Software Foundation If the Document does not specify a version number of this License you may choose any version ever published not as a draft by the Free Software Foundation 22 Publication Harvester and Colleague Generator Software Requirements Specification 5 Revision History Date Author Description 19 Dec 2007 Andrew Stellman Created initial version 10 Jan 2008 Andrew Stellman Fixed screenshots filled out overview and compelted
5. Weights File box to locate it The Colleagues report is exactly the same as the People report in the Publication Harvester By default it only contains summary rows for publication type bins 1 2 3 Field Type Description setnb key Text Colleague unique identifier year key Number Year of publication pubcount Number Total nb of pubs in year bins I II III weghtd_pubcount Number Weighted total nb of pubs in year bins HIHI pubcount_pos Number Total nb of pubs in year bins I II III 1 author wghtd_pubcount_posl Number Weighted total nb of pubs in year bins I II III 1 author pubcount_posN Number Total nb of pubs in year bins I II III last author wghtd_pubcount_posN Number Weighted total nb of pubs in year bins I II II last author pubcount_posM Number Total nb of pubs in year bins I I II middle author weghtd_pubcount_posM Number Weighted total nb of pubs in year bins I II III middle author pubcount_posNTL Number Total nb of pubs in year bins I II II next to last author weghtd_pubcount_posNTL Number Weighted total nb of pubs in year bins I II III next to last author pubcount_pos2 Number Total nb of pubs in year bins I II III 2 author wghtd_ pubcount_pos2 Number Weighted total nb of pubs in year bins I II III 2 author You can add additional sections for additional publ
6. modification Examples of transparent image formats include PNG XCF and JPG Opaque formats include proprietary formats that can be read and edited only by proprietary word processors SGML or XML for which the DTD and or processing tools are not generally available and the machine generated HTML PostScript or PDF produced by some word processors for output purposes only The Title Page means for a printed book the title page itself plus such following pages as are needed to hold legibly the material this License requires to appear in the title page For works in formats which do not have any title page as such Title Page means the text near the most prominent appearance of the work s title preceding the beginning of the body of the text A section Entitled XYZ means a named subunit of the Document whose title either is precisely XYZ or contains XYZ in parentheses following text that translates XYZ in another language Here XYZ stands for a specific section name mentioned below such as Acknowledgements Dedications Endorsements or History To Preserve the Title of such a section when you modify the Document means that it remains a section Entitled XYZ according to this definition The Document may include Warranty Disclaimers next to the notice which states that this License applies to the Document These Warranty Disclaimers are considered to be included by reference in this License but only as regards disclaiming warranti
7. paper where the star was second author that year Nbcoauth_ NTLI number Number of times the colleague appears as next to last author on a paper where the star was first author that year Weghtd Nbcoauth NTL1 number Weighted number of times the colleague appears as next to last author on a paper where the star was first author that year 13 Publication Harvester and Colleague Generator Software Requirements Specification Nbcoauth_1NTL number Number of times the colleague appears as first author on a paper where the star was next to last author that year Weghtd_ Nbcoauth INTL number Weighted number of times the colleague appears as first author on a paper where the star was next to last author that year Nbcoauth NTLM number Number of times the colleague appears as next to last author on a paper where the star was in the middle not 2 author that year Weghtd Nbcoauth NTLM number Weighted number of times the colleague appears as next to last author on a paper where the star was in the middle not 2 author that year Nbcoauth_MNTL number Number of times the colleague appears as middle author not 2 author on a paper where the star was next to last author that year Weghtd Nbcoauth MNTL number Weighted number of times the colleague appears as middle author not 2 author on a paper where the star was next to last author that year Nbcoauth_ NTLL number Number of times t
8. the Star Colleague Pairs box The colleagues are not entirely removed from the database they are just disassociated from the stars That way if one person is a colleague to two stars his publications remain in the database 3 3 Generate the colleague reports Once all colleagues are harvested and false colleagues are removed click the Step 5 button to generate the reports It brings up this dialog box 10 Publication Harvester and Colleague Generator Software Requirements Specification Generate Harvesting Reports BR as oid ad Colleagues Report Sections V Colleagues colleagues csv 1 2 3 V Publications publications csv Mv Star Colleagues starcolleagues csv Section to add Add Specify a Folder to Write To C Documents and Settings Default User Desktop Journal Weights File C Documents and Settings Default User Desktop sample JIFs xls You can specify the names of the three reports using the boxes They re all generated in the same folder use the first button to specify the folder to write to If any of the files exist in the folder already use the Overwrite existing report or Continue where report ends radio buttons to specify whether to overwrite or continue the report You ll need to specify a Journal Weights JIF file for the Colleagues report This is the same JIF file that was used with the Publication Harvester Click the button next to the Journal
9. the terms of this License Such a notice grants a world wide royalty free license unlimited in duration to use that work under the conditions stated herein The Document below refers to any such manual or work Any member of the public is a licensee and is addressed as you You accept the license if you copy modify or distribute the work in a way requiring permission under copyright law A Modified Version of the Document means any work containing the Document or a portion of it either copied verbatim or with modifications and or translated into another language A Secondary Section is a named appendix or a front matter section of the Document that deals exclusively with the relationship of the publishers or authors of the Document to the Document s overall subject or to related matters and contains nothing that could fall directly within that overall subject Thus if the Document is in part a textbook of mathematics a Secondary Section may not explain any mathematics The relationship could be a matter of historical connection with the subject or with related matters or of legal commercial philosophical ethical or political position regarding them The Invariant Sections are certain Secondary Sections whose titles are designated as being those of Invariant Sections in the notice that says that the Document is released under this License If a section does not fit the above definition of Secondary then it is not allowed to be d
10. to these copies of the Document then if the Document is less than one half of the entire aggregate the Document s Cover Texts may be placed on covers that bracket the Document within the aggregate or the electronic equivalent of covers if the Document is in electronic form Otherwise they must appear on printed covers that bracket the whole aggregate 8 TRANSLATION Translation is considered a kind of modification so you may distribute translations of the Document under the terms of section 4 Replacing Invariant Sections with translations requires special permission from their copyright holders but you may include translations of some or all Invariant Sections in addition to the original versions of these Invariant Sections You may include a translation of this License and all the license notices in the Document and any Warranty Disclaimers provided that you also include the original English version of this License and the original versions of those notices and disclaimers In case of a disagreement between the translation and the original version of this License or a notice or disclaimer the original version will prevail Ifa section in the Document is Entitled Acknowledgements Dedications or History the requirement section 4 to Preserve its Title section 1 will typically require changing the actual title 9 TERMINATION You may not copy modify sublicense or distribute the Document except as expressly provided for under this
11. 0 Alice Carol Effie 1992 0 1 1 0 0 0 Alice Carol Effie 1993 1 2 1 0 0 0 Alice Carol Effie 1994 0 2 1 0 0 0 Alice Carol Effie 1995 0 2 1 2 0 0 18 Publication Harvester and Colleague Generator Software Requirements Specification 4 4 Restricting the Report to a List of Colleagues A SQL database generated by the Publication Harvester and SC Gen can contain a very large number of colleagues and most of those colleagues may be irrelevant to the researcher generating the reports To remedy this the researcher may optionally specify a list of colleagues If this list is specified then the software only generates the social network for those colleagues and the final report contains only those colleagues The list of colleagues is text file that contains the setnb values for each colleague to include in the report with one setnb per line For example if you want to generate a report that only includes Alice Justin and Efffie you d specify a text file with their setnbs on each line Alice Justin Effie If this file is specified then the software will only generate a report for Alice Justin and Effie However the software will not generate any report rows for any setnb that is not actually contained in the database 4 5 Fault tolerance The Social Networking report generator is capable of producing extremely long reports which may take a long time to produce If a long run were to be interrupted by a power failure for exampl
12. 08 11 29 35 AM Finding Doe X0000001 1 of 2 1 10 2008 11 29 35 AM Finding Smith X0000002 2 of 2 Publication Harvester and Colleague Generator Software Requirements Specification Once the potential colleagues are found and added to the database each colleague s publications need to be harvested There are two ways to do that If you have a lot of colleagues whose publications you ll be repeatedly harvesting you can create a separate Publication Harvester input file with those colleagues and add them to a separate database on the same MySQL server Once you ve got that you can click the Copy Publications from Another Database button which brings up this window Copy Colleague Publications x Select a database to copy from Pre harvested Colleagues v Copy Publications Select the database that contains the publications to copy When you click the Copy Publications button the program will copy the publications from one database to the other It will mark the colleagues for which the publications were copied as harvested that way when you retrieve the publications later for the remaining colleagues the system won t take the time to download and process those colleagues publications It s much faster to copy publications from another database than it is to download them from PubMed so this can save a lot of time You can copy publications repeatedly from several other databases
13. 1 2008 4 19 05 PM Removed 8 false colleagues 2007 Stellman and Greene Consulting LLC http www stellman greene com Permission is granted to copy distribute and or modify this document under the terms of the GNU Free Documentation License Version 1 2 or any later version published by the Free Software Foundation with no Invariant Sections no Front Cover Texts and no Back Cover Texts A copy of the license is included in the section entitled GNU Free Documentation License Publication Harvester and Colleague Generator Software Requirements Specification Table of Contents 1 Introduction 1 1 Purpose 1 2 Scope 1 3 System Overview 1 4 References 2 Installation 2 1 Before you start 2 2 Install the SC Gen and Social Networking software 2 3 Overview of the SC Gen software 3 Using the SC Gen software 3 1 Specify the Roster File 3 2 Generate Colleagues 3 3 Generate the colleague reports 4 Generating the Social Networking Report 4 1 Before you can generate the Social Networking report 4 2 The second degree social network 4 3 Generating the social network report 4 4 Restricting the Report to a List of Colleagues GNU Free Documentation License 5 Revision History we b amp w ww Ww U KR HK A A 7 10 15 16 16 17 19 20 23 Publication Harvester and Colleague Generator Software Requirements Specification 1 Introduction 1 1 Purpose The purpose of this document is
14. ICATIONS You may copy and distribute a Modified Version of the Document under the conditions of sections 2 and 3 above provided that you release the Modified Version under precisely this License with the Modified Version filling the role of the Document thus licensing distribution and modification of the Modified Version to whoever possesses a copy of it In addition you must do these things in the Modified Version e A Use in the Title Page and on the covers if any a title distinct from that of the Document and from those of previous versions which should if there were any be listed in the History section of the Document You may use the same title as a previous version if the original publisher of that version gives permission s B List on the Title Page as authors one or more persons or entities responsible for authorship of the modifications in the Modified Version together with at least five of the principal authors of the Document all of its principal authors if it has fewer than five unless they release you from this requirement s C State on the Title page the name of the publisher of the Modified Version as the publisher s D Preserve all the copyright notices of the Document bed E Add an appropriate copyright notice for your modifications adjacent to the other copyright notices y F Include immediately after the copyright notices a license notice giving the public permission to use the Modified Version under the ter
15. Missing Colleague Publications Colleagues Harvested l Step 5 Remove False Colleagues J Colleague Publications Downloaded i Step 6 Generate Reports Unique Colleagues Found Languages list of Medline language abbreviations separated by commas blank for no restriction jeng Allowed publication type categories 123 Log file C Documents and Settings Andrew My Documents Visual Studio 2008 Projects Pub Open in Notepad Log 1 11 2008 4 19 05 PM Removed false colleague C0000003 1 11 2008 4 19 05 PM Removed false colleague C0000008 1 11 2008 4 19 05 PM Removed false colleague C0000009 1 11 2008 4 19 05 PM Removed false colleague C0000010 1 11 2008 4 19 05 PM Removed false colleague C0000013 1 11 2008 4 19 05 PM Removed false colleague C0000014 1 11 2008 4 19 05 PM Removed 8 false colleagues a There are many cases where you ll find roster matches that don t actually represent real colleagues For example there could be two John Smiths with different PubMed queries If the star has a publication with author SMITH J both roster rows will be matched But once the colleagues publications are harvested it s possible to check each colleague s publication list against the star s publication list If there are no publications in common then the colleague is a spurious colleague Step 4 removes those false colleagues from the database and updates the Stars with Colleagues box and
16. SA Everyone is permitted to copy and distribute verbatim copies of this license document but changing it is not allowed 0 PREAMBLE The purpose of this License is to make a manual textbook or other functional and useful document free in the sense of freedom to assure everyone the effective freedom to copy and redistribute it with or without modifying it either commercially or noncommercially Secondarily this License preserves for the author and publisher a way to get credit for their work while not being considered responsible for modifications made by others This License is a kind of copyleft which means that derivative works of the document must themselves be free in the same sense It complements the GNU General Public License which is a copyleft license designed for free software We have designed this License in order to use it for manuals for free software because free software needs free documentation a free program should come with manuals providing the same freedoms that the software does But this License is not limited to software manuals it can be used for any textual work regardless of subject matter or whether it is published as a printed book We recommend this License principally for works whose purpose is instruction or reference 1 APPLICABILITY AND DEFINITIONS This License applies to any manual or other work in any medium that contains a notice placed by the copyright holder saying it can be distributed under
17. SC Gen and the Social Networking Report User Manual SC Gen v1 0 14 and Social Networking Report v1 0 5 SC Gen Stars Colleague Generator ODBC Data Source Name Publication Harvester Roster File C Documents and Settings Andrew Desktop sample roster csv J Database Status Tables Created k People People Harvested Publications Found True 2 2 7 People With Errors People Not Harvested Colleagues With Errors 0 0 0 Step 1 Read the Roster file Roster Rows Step 2 Find the Potential Colleagues Stars with Colleagues Step 3 Copy Publications from Another Database Star Colleague Pairs Found Step 4 Retrieve Missing Colleague Publications Colleagues Harvested 1 Step 5 Remove False Colleagues Colleague Publications Downloaded Step 6 Generate Reports Unique Colleagues Found Languages list of Medline language abbreviations separated by commas blank for no restriction eng Allowed publication type categories 123 Log fe oa en a C Documents and Settings Andrew My Documents Visual Studio 2008 Projects Pub Open in Notepad Log 1 11 2008 4 19 05 PM Removed false colleague C0000003 a 1 11 2008 4 19 05 PM Removed false colleague C0000008 a 1 11 2008 4 19 05 PM Removed false colleague C0000009 1 11 2008 4 19 05 PM Removed false colleague C0000010 1 11 2008 4 19 05 PM Removed false colleague C0000013 1 11 2008 4 19 05 PM Removed false colleague C0000014 1 1
18. agency Text Agency who awarded the grant publication _type Text Publication Type from PubMed The Star Colleagues report contains a set of rows for each colleague and star Each of these sets of rows consists of one row for each year that the star and colleague coauthored at least one paper together This report will exclude any line for which there are no publications in common for the star and colleague for that year i e nbcoauth1 0 So if a star and colleague only coauthored in 1976 and 1984 there will be two rows in this report for them The report is grouped by star colleague and year with various aggregations performed on the colleague s publications for that year If the same colleague is a colleague of two different stars then there will be two different groups in the report for that colleague one for the first star and one for the second star A journal weights file must be provided in order to calculate the weighted publication counts the software must prompt the user for the location of this file before the reports are run Field Type Description setnb key Text Colleague unique identifier star_setnb key Text Star colleague unique identifier year key Number Year of publication Nbcoauth1 Number Total number of coauthorships any pos to any pos Wghtd Nbcoauth1 Number Weighted number of coauthorships any pos to any pos Nbcoauth2 Number Total numbe
19. base http dev mysql com doc refman 5 0 en upgrading to arch html Once you have the two databases the regular database and the square database you re ready to use the Social Networking report software to generate the report 4 2 The second degree social network The purpose of the Social Networking Report is to generate a report that will be used to statistically test social networking hypotheses using the data gathered the Publication Harvester and SC Gen It generates a second degree social network using two databases generated by Publication Harvester and SC Gen The second degree database is a normal database generated by SC Gen while the first degree database should be a square database that was generated by harvesting the same people that were used to harvest the first database The difference is that instead of using the full roster of potential colleagues its roster only contains the people in the original people list that way it will only find colleagues who are also on the list Once the two databases are created the social network can be found for each colleague Here s a typical colleague s social network 16 Publication Harvester and Colleague Generator Software Requirements Specification Malloy 2nd degree star 1992 gt Joe 24 degree star 1996 Carol foo Lisa a 1 Degree Star jog lal 2nd degree star 1991 1993
20. d formatted name optional e search namel text length 20 PubMed formatted name e search name2 text length 20 PubMed formatted name optional e search name3 text length 20 PubMed formatted name optional e search name 4 text length 20 PubMed formatted name optional e query text length 244 A search query which will be used to retrieve publications from Pubmed The matchnamel and matchname2 columns are used to match the person in the roster to a person s publication If either of these names shows up in the list of authors in a person s publication then the person is a colleague matchname2 can be empty in which case the software only looks for matches against matchname1 The searchname1 through searchname4 columns are used to look in the results of a PubMed query to find a colleague s publications If any of those names matches a name in the author list of a returned citation then that colleague is an author of the publication searchname2 through searchname4 can be empty the software will only search on the provided names Each of the name columns contain a name in the same format as the author list in a PubMed citation e g for Robert E Elston namel might contain ELSTON RE The search name through search_name4 columns are used to search PubMed and retrieve citations in the same way as in the People file see the Publication Harvester SRS A sample roster file can be downloaded from t
21. e it would be frustrating and time consuming to have to regenerate the report rows that were already produced To avoid this problem fault tolerance is built into the report generator To resume a partially generated report just select the report file that you began The software will first warn you that you have selected an existing file It will then display a prompt Continue existing report file 9 The report file exists Continue from where the previous report left off 1 7 Click No to overwrite the report and restart it from the beginning Co JC If you select Yes the report generator will rename the existing file adding bak to the end of the filename If will then create a new file and copy all of the rows out of the old one except for the block of rows for the last colleague in the file because if the report generator was previously interrupted it may not have finished writing that colleague s network It will then skip any colleague which was copied from existing file If you select No the report generator will delete the existing file If you select Cancel then it will cancel the operation and not write or change any files 19 Publication Harvester and Colleague Generator Software Requirements Specification GNU Free Documentation License Version 1 2 November 2002 Copyright C 2000 2001 2002 Free Software Foundation Inc 51 Franklin St Fifth Floor Boston MA 02110 1301 U
22. eagues contains the number of distinct stars that it finds in the StarColleagues table that s the number of stars that have at least one colleague The Star Colleague Pairs Found contains the number of pairs of stars and colleagues And the Unique Colleagues Found box contains the total number of unique colleagues across all stars in the entire database SC Gen Stars Colleague Generator ODBC Data Source Name Publication Harvester Roster File C Documents and Settings Andrew Desktop sample roster csv Database Status Tables Created People People Harvested Publications Found True 2 2 145 People With Errors People Not Harvested Colleagues With Errors 0 0 lo Step 1 Read the Roster file Roster Rows Step 2 Find the Potential Colleagues Stars with Colleagues Step 3 Copy Publications from Another Database Star Colleague Pairs Found 1 Step 4 Retrieve Missing Colleague Publications Colleagues Harvested Colleague Publications Downloaded Step 5 Generate Reports Unique Colleagues Found Languages list of Medline language abbreviations separated by commas blank for no restriction eng Allowed publication type categories 123 Log file C Documents and Settings Andrew My Documents Visual Studio 2008 Projects Pub Open in Notepad Log 1 10 2008 11 29 30 AM Read 16 from C Documents and Settings Andrew Desktop sample roster csv 1 10 20
23. es any other implication that these Warranty Disclaimers may have is void and has no effect on the meaning of this License 2 VERBATIM COPYING You may copy and distribute the Document in any medium either commercially or noncommercially provided that this License the copyright notices and the license notice saying this License applies to the Document are reproduced in all copies and that you add no other conditions whatsoever to those of this License You may not use technical measures to obstruct or control the reading or further copying of the copies you make or distribute However you may accept compensation in exchange for copies If you distribute a large enough number of copies you must also follow the conditions in section 3 You may also lend copies under the same conditions stated above and you may publicly display copies 3 COPYING IN QUANTITY If you publish printed copies or copies in media that commonly have printed covers of the Document numbering more than 100 and the Document s license notice requires Cover Texts you must enclose the copies in covers that carry clearly and legibly all these Cover Texts Front Cover Texts on the front cover and Back Cover Texts on the back cover Both covers must also clearly and legibly identify you as the publisher of these copies The front cover 20 Publication Harvester and Colleague Generator Software Requirements Specification must present the full title with all words of t
24. esignated as Invariant The Document may contain zero Invariant Sections If the Document does not identify any Invariant Sections then there are none The Cover Texts are certain short passages of text that are listed as Front Cover Texts or Back Cover Texts in the notice that says that the Document is released under this License A Front Cover Text may be at most 5 words and a Back Cover Text may be at most 25 words A Transparent copy of the Document means a machine readable copy represented in a format whose specification is available to the general public that is suitable for revising the document straightforwardly with generic text editors or for images composed of pixels generic paint programs or for drawings some widely available drawing editor and that is suitable for input to text formatters or for automatic translation to a variety of formats suitable for input to text formatters A copy made in an otherwise Transparent file format whose markup or absence of markup has been arranged to thwart or discourage subsequent modification by readers is not Transparent An image format is not Transparent if used for any substantial amount of text A copy that is not Transparent is called Opaque Examples of suitable formats for Transparent copies include plain ASCII without markup Texinfo input format LaTeX input format SGML or XML using a publicly available DTD and standard conforming simple HTML PostScript or PDF designed for human
25. he colleague appears as next to last author on a paper where the star was last author that year Weghtd Nbcoauth NTLL number Weighted number of times the colleague appears as next to last author on a paper where the star was last author that year Nbcoauth_LNTL number Number of times the colleague appears as last author on a paper where the star was next to last author that year Weghtd Nbcoauth LNTL number Weighted number of times the colleague appears as last author on a paper where the star was next to last author that year Frst_collab_year Number Year of first collaboration with the star any position to any position Last_collab_year Number Year of last collaboration with the star any position to any position 14 Publication Harvester and Colleague Generator Software Requirements Specification 4 Generating the Social Networking Report The purpose of the Social Networking Report is to generate a data that will be used to statistically test social networking hypotheses using the data gathered the Publication Harvester and SC Gen It creates a two degree social network each colleague is connected to several stars and each star is connected to additional stars For additional information on the social networking including how the social network is defined see the Social Networking requirements http stellman greene com SCGen SRS_SocialNetworking doc it also defines the formats of the report file and the co
26. he following URL http stellman greene com SCGen sample roster csv Publication Harvester and Colleague Generator Software Requirements Specification 3 2 Generate Colleagues Before you can generate colleagues you ll need to create and populate a database using the Publication Harvester Once that database is created and populated start the SC Gen software and select the ODBC data source name you used with the Publication Harvester If you click the button next to that field it will pop up the ODBC Data Source Administrator Click on the button next to the Roster File field and browse to the Roster Your SC Gen window will look like this SC Gen Stars Colleague Generator ODBC Data Source Name a GJ About Roster File SC Gen C Documents and Settings Andrew Desktop sample roster csv J Database Status Tables Created People People Harvested Publications Found False 0 fo 0 People With Errors People Not Harvested Colleagues With Errors lo 0 0 Step 1 Read the Roster file Roster Rows notloaded Stars with Colleagues Star Colleague Pairs Found Colleagues Harvested Colleague Publications Downloaded Step 6 Generate Reports Unique Colleagues Found Languages list of Medline language abbreviations separated by commas blank for no restriction eng Allowed publication type categories _ 1 23 Log file C Documents and Settings Andrew My Documents Visua
27. he title equally prominent and visible You may add other material on the covers in addition Copying with changes limited to the covers as long as they preserve the title of the Document and satisfy these conditions can be treated as verbatim copying in other respects If the required texts for either cover are too voluminous to fit legibly you should put the first ones listed as many as fit reasonably on the actual cover and continue the rest onto adjacent pages If you publish or distribute Opaque copies of the Document numbering more than 100 you must either include a machine readable Transparent copy along with each Opaque copy or state in or with each Opaque copy a computer network location from which the general network using public has access to download using public standard network protocols a complete Transparent copy of the Document free of added material If you use the latter option you must take reasonably prudent steps when you begin distribution of Opaque copies in quantity to ensure that this Transparent copy will remain thus accessible at the stated location until at least one year after the last time you distribute an Opaque copy directly or through your agents or retailers of that edition to the public It is requested but not required that you contact the authors of the Document well before redistributing any large number of copies to give them a chance to provide you with an updated version of the Document 4 MODIF
28. ication types by typing the section to add and clicking the Add button For example you can specify that the report also contain information that only includes data from bin 2 by adding 2 to the sections This will add additional columns to the report there will be a set of columns added for every section you add using the Add button The 11 Publication Harvester and Colleague Generator Software Requirements Specification names will be altered to indicate which section they belong to 2pubcount wghtd_2pubcount 2pubcount_posl wghtd 2pubcount pos etc The Publications report contains one row for each colleague s publications Each colleague is identified by the unique identifier Setnb There is one row in this report per each colleague s publication Field Type Description setnb key Text Star unique identifier pmid key Number Unique article identifier Journal_name Text Name of journal Year Number Year of publication Month text Month of publication Day Number Day of publication Title Text Article title Volume Text volume number of the journal in which the article was published Issue Text Issue in which the article was published Position Number Position in authorship list for the colleague Nbauthors Number Number of coauthors including star Bin Number From I to IV Pages Text Page numbers grant id Text Grant number grant
29. ide net to find as many colleagues as possible for each person in the Publication Harvester input file to generate a large second degree social network However the first degree social network is created by starting with the colleagues in the first database Each of those colleagues is associated with a person in the original input file Some are associated with more than one person in that case they re treated as two separate cases and have two separate sets of rows in the social networking report By feeding a square database to SC Gen when you generate the first degree database you create a smaller list of potential colleagues Once all of the people are found for each colleague then their colleagues need to be found But those colleagues aren t found in the original database Instead the program searches for second degree colleagues using the people in the original input file that was used to create the Publication Harvester database To do this you ll create a square roster which is just a roster that contains the people in the original input file You ll use the Publication Harvester to create a database with the same input file you used for the regular database Then you ll use SC Gen to find the colleagues in the square database using the square roster file instead of the one you used for the regular database Note You don t have to re harvest the publications to create the square database You can just copy the MySQL data
30. l Studio 2008 Projects Pub Log Click the button labeled Step 1 Read the Roster file SC Gen will read the roster file into memory It also creates an XML file in the same folder that contains the same information as the roster For a very large roster file it s faster to load the XML file than it is to load the CSV file The XML file will have the same name as the CSV file with xml added to the end sample roster csv xml The number of rows in the roster will be displayed in the Roster Rows box Once the roster is read the button labeled Step 2 Find the Potential Colleagues will be enabled Publication Harvester and Colleague Generator Software Requirements Specification SC Gen Stars Colleague Generator ODBC Data Source Name Publication Harvester Roster File C Documents and Settings Andrew Desktop sample roster csv Database Status Tables Created People People Harvested d Publications Found True 2 2 _ People With Errors People Not Harvested Colleagues With Errors 0 0 lo Step 1 Read the Roster file Roster Rows 16 Step 2 Find the Potential Colleagues Stars with Colleagues 0 Star Colleague Pairs Found Colleagues Harvested l Jes Colleague Publications Downloaded Step 6 Generate Reports Unique Colleagues Found Languages list of Medline language abbreviations separated by commas blank for no restrictio
31. les Section numbers or the equivalent are not considered part of the section titles bg M Delete any section Entitled Endorsements Such a section may not be included in the Modified Version z N Do not retitle any existing section to be Entitled Endorsements or to conflict in title with any Invariant Section O Preserve any Warranty Disclaimers If the Modified Version includes new front matter sections or appendices that qualify as Secondary Sections and contain no material copied from the Document you may at your option designate some or all of these sections as invariant To do this add their titles to the list of Invariant Sections in the Modified Version s license notice These titles must be distinct from any other section titles You may add a section Entitled Endorsements provided it contains nothing but endorsements of your Modified Version by various parties for example statements of peer review or that the text has been approved by an organization as the authoritative definition of a standard You may add a passage of up to five words as a Front Cover Text and a passage of up to 25 words as a Back Cover Text to the end of the list of Cover Texts in the Modified Version Only one passage of Front Cover Text and one of Back Cover Text may be added by or through arrangements made by any one entity If the Document already includes a cover text for the same cover previously added by you or by arrangement made by the same entit
32. lleagues file You can use the Social Networking program to generate this second degree network 1 Specify the regular and square databases that have already been generated using Publication Harvester and SC Gen 2 By default the program generates the complete social network for every colleague in the database But you can specify a list of colleagues to make the software generate a subset of the data 3 The program searches the database and creates a report file that can be used for statistical analysis The Social Networking Report needs two databases a database that contains the colleagues and defines the first degree network and a database that defines the second degree network Both databases must be on the same server To specify the databases first select an ODBC data source Social Networking Report ODBC Data Source Name Publication Harvester First Degree Database Second Degree Database harvested_colleagues v square_database Report file to write C Documents and Settings Andrew My Documents socialreportcsv File with list of colleagues to search for leave empty to search for all colleagues C Documents and Settings Andrew My Documents colleagues tt J Write the Report Once the data source is selected the First Degree and Second Degree Database dropdown lists are populated with all of the databases on the server Select the two databases After the databases are selected click the button
33. ms of this License in the form shown in the Addendum below s G Preserve in that license notice the full lists of Invariant Sections and required Cover Texts given in the Document s license notice H Include an unaltered copy of this License d I Preserve the section Entitled History Preserve its Title and add to it an item stating at least the title year new authors and publisher of the Modified Version as given on the Title Page If there is no section Entitled History in the Document create one stating the title year authors and publisher of the Document as given on its Title Page then add an item describing the Modified Version as stated in the previous sentence e J Preserve the network location if any given in the Document for public access to a Transparent copy of the Document and likewise the network locations given in the Document for previous versions it was based on These may be placed in the History section You may omit a network location for a work that was published at least four years before the Document itself or if the original publisher of the version it refers to gives permission K For any section Entitled Acknowledgements or Dedications Preserve the Title of the section and preserve in the section all the substance and tone of each of the contributor acknowledgements and or dedications given therein bd L Preserve all the Invariant Sections of the Document unaltered in their text and in their tit
34. n eng Allowed publication type categories 123 Log file C Documents and Settings Andrew My Documents Visual Studio 2008 Projects Pub Open in Notepad Log 1 11 2008 4 16 04 PM Read 16 from C Documents and Settings Andrew Desktop sample roster csv Click the Step 2 button to tell SC Gen to read the database and find the potential colleagues The software will add additional tables to the database to hold the colleague information If you click the Step 2 button on a database that already contains colleagues that were found it ll display a warning box Re find Colleagues x Colleagues have already been found Are you sure you want to re find them or continue the previous search If you click Yes you can choose to either continue the previous colleague search or reset the database and find new colleagues Publication Harvester and Colleague Generator Software Requirements Specification Continue from previous search x Should the colleague search continue where it was previously left off Click No to reset the database and start finding new colleagues Those two windows will only appear if there are already colleagues in the database If you re using a clean Publication Harvester database that s never had colleagues generated those windows will not pop up Once the potential colleagues are found the system will show data in three additional boxes Stars with Coll
35. next to the report file box to specify the name of the report file to write Click the Write the Report button to write the report to the file You can optionally specify a file that contains a list of setnb values of the colleagues to include in the report If this file isn t specified all of the colleagues will be included in the report If it is specified then only the colleagues whose setnbs appear in the file will be included in the report 15 Publication Harvester and Colleague Generator Software Requirements Specification 4 1 Before you can generate the Social Networking report The Social Networking report generator requires two databases that reside on the same server The first database is a standard database that has been generated by the Publication Harvester and SC Gen with all of the colleagues generated If you have followed all of the steps in this manual through the end of section 3 then you have created the first database The second database is also created by the Publication Harvester and SC Gen using the same Publication Harvester input file The difference is that for the first degree database you ll use a square roster file when you use SC Gen to generate the colleagues while you ll use a larger roster to generate the second degree database Typically your roster file for the second degree database will be much larger than the input file for the Publication Harvester because you usually want to cast a w
36. ns Entitled Acknowledgements and any sections Entitled Dedications You must delete all sections Entitled Endorsements 6 COLLECTIONS OF DOCUMENTS 21 Publication Harvester and Colleague Generator Software Requirements Specification You may make a collection consisting of the Document and other documents released under this License and replace the individual copies of this License in the various documents with a single copy that is included in the collection provided that you follow the rules of this License for verbatim copying of each of the documents in all other respects You may extract a single document from such a collection and distribute it individually under this License provided you insert a copy of this License into the extracted document and follow this License in all other respects regarding verbatim copying of that document 7 AGGREGATION WITH INDEPENDENT WORKS A compilation of the Document or its derivatives with other separate and independent documents or works in or on a volume of a storage or distribution medium is called an aggregate if the copyright resulting from the compilation is not used to limit the legal rights of the compilation s users beyond what the individual works permit When the Document is included in an aggregate this License does not apply to the other works in the aggregate which are not themselves derivative works of the Document If the Cover Text requirement of section 3 is applicable
37. nstaller is finished it will run the software it installed It will appear in the Start menu listed under Publication Harvester In addition there are sample files that can be downloaded from the SC Gen website e sample roster csv sample input roster file that contains potential colleagues e sample JIFs xls sample JIF file for generating reports e sample square roster csv sample square roster file generated to match the Publication Harvester sample input file e sample input xls sample input People file you can use with the Publication Harvester e sample colleagues txt sample colleague file used by the Social Networking Report 2 3 Overview of the SC Gen software The purpose of SC Gen is to identify the colleagues of people who were harvested using the Publication Harvester The Publication Harvester starts with a list of people finds each person s publication citations using PubMed and saves them in a MySQL database SC Gen picks up where Publication Harvester left off by reading the data for the people and their publications from the database 1 The software reads a roster file that contains information for potential colleagues 2 The software generates colleagues by searching through the publications for each person in the Publication Harvester database and comparing the coauthors to the people in the roster file A person s colleague is someone who coauthored a publication with that pe
38. ow per each year in the range from the earliest publication to the latest publication For example the earliest publication in the Alice Carol Bob combination is 1991 and the latest is 2003 so for these three people there will be 13 rows in the report For each row there are three relationships to measure colleague and 1 degree star 1 degree star and 2 degree star colleague and 2 degree star This last measurement is important in order to answer research questions about whether being in the same network as a star would predict a 2 degree colleague s work It also may be useful to limit a network only to colleagues who never end up working with 2 degree stars or to years that predate colleague 2 degree star coauthorships 17 Publication Harvester and Colleague Generator Software Requirements Specification Each of the three relationships in a given year is measured using stock and flow The flow measurement is the number of publications in coauthored by the two people in that year The stock measurement is the cumulative number of publications coauthored by the two people in that year or any earlier year The report will be a comma delimited text CSV file with a header row and the following columns Field Type Description setnb0 key Text Colleague unique identifier setnb1 key Text 1 degree star colleague unique identifier setnb2 key Text oe degree star colleague unique identifie
39. r year key Number Year flow0tol Number Flow for colleague to 1 degree star stkOto1 Number Stock for colleague to 1 degree star flow1to2 Number Flow for 1 degree star to 2 degree star stk1to2 Number Stock for 1 degree star to oa degree star flow0to2 Number Flow for colleague to pu degree star stk0to2 Number Stock for colleague to on degree star In the social network shown in the above diagram there are 14 different combinations of colleague 1 degree star and 2 degree star in this network The following rows will be generated for the Alice Justin John combination setnb0 setnb1 setnb2 year flow0tol stk0tol flowlto2 stkito2 flow0to2 stk0to2 Alice Justin John 1995 1 1 0 0 0 0 Alice Justin John 1996 1 1 1 1 Alice Justin John 1997 1 1 0 1 0 0 Alice Justin John 1998 1 1 0 1 0 0 Alice Justin John 1999 1 1 1 2 0 0 Alice Justin John 2000 1 1 0 2 0 0 Alice Justin John 2001 1 1 0 2 0 0 Alice Justin John 2002 1 1 0 2 1 1 Alice Justin John 2003 1 1 0 2 1 1 Alice Justin John 2004 1 1 0 2 1 1 Alice Justin John 2005 1 1 1 3 1 1 The following rows will be generated for the Alice Carol Effie combination setnb0 setnb1 setnb2 year flow0tol stk0tol flowlto2 stkito2 flow0to2 stk0to2 Alice Carol Effie 1985 0 0 1 1 0 0 Alice Carol Effie 1986 0 0 1 0 0 0 Alice Carol Effie 1987 0 0 1 0 0 0 Alice Carol Effie 1988 0 0 1 0 0 0 Alice Carol Effie 1989 0 0 1 0 0 0 Alice Carol Effie 1990 0 0 1 0 0 0 Alice Carol Effie 1991 1 1 1 0 0
40. r of coauthorships either star or colleague 1 or last Wghtd_ Nbcoauth2 Number Weighted number of coauthorships either star or colleague 1 or last Nbcoauth_1L number Number of times the colleague appears as first author on a paper where the star was last author that year Weghtd_ Nbcoauth_1L number Weighted number of times the colleague appears as first author on a paper where the star was last author that year Nbcoauth L1 number Number of times the colleague appears as last author on a paper where the star was first author that year Weghtd Nbcoauth L1 number Weighted number of times the colleague appears as last author on a 12 Publication Harvester and Colleague Generator Software Requirements Specification paper where the star was first author that year Nbcoauth_1M number Number of times the colleague appears as first author on a paper where the star was in the middle that year Weghtd Nbcoauth_1M number Weighted number of times the colleague appears as first author on a paper where the star was in the middle that year Nbcoauth M1 number Number of times the colleague appears as in the middle on a paper where the star was first author that year Wghtd_Nbcoauth_M1 number Weighted number of times the colleague appears as in the middle on a paper where the star was first author that year Nbcoauth MM number Number of times the colleague appea
41. r of times the colleague appears as second author on a paper where the star was in the middle not NTL that year Nbcoauth_M2 number Number of times the colleague appears as middle author not NTL ona paper where the star was second author that year Weghtd Nbcoauth_M2 number Weighted number of times the colleague appears as middle author not NTL on a paper where the star was second author that year Nbcoauth_2L number Number of times the colleague appears as second author on a paper where the star was last author that year Weghtd_ Nbcoauth 2L number Weighted number of times the colleague appears as second author on a paper where the star was last author that year Nbcoauth_L2 number Number of times the colleague appears as last author on a paper where the star was second author that year Wghtd Nbcoauth L2 number Weighted number of times the colleague appears as last author on a paper where the star was second author that year Nbcoauth_2NTL number Number of times the colleague appears as second author on a paper where the star was next to last author that year Wghtd_ Nbcoauth 2NTL number Weighted number of times the colleague appears as second author on a paper where the star was next to last author that year Nbcoauth_NTL2 number Number of times the colleague appears as next to last author on a paper where the star was second author that year Weghtd_ Nbcoauth NTL2 number Weighted number of times the colleague appears as next to last author on a
42. rs as in the middle on a paper where the star was in the middle that year Wghtd_Nbcoauth MM number Weighted number of times the colleague appears as in the middle on a paper where the star was in the middle that year Nbcoauth LM number Number of times the colleague appears as last author on a paper where the star was in the middle that year Wghtd_Nbcoauth_ LM number Weighted number of times the colleague appears as last author on a paper where the star was in the middle that year Nbcoauth ML number Number of times the colleague appears as in the middle on a paper where the star was last author that year Wghtd_Nbcoauth_ ML number Weighted number of times the colleague appears as in the middle on a paper where the star was last author that year Nbcoauth 21 number Number of times the colleague appears as second author on a paper where the star was first author that year Wghtd_Nbcoauth_21 number Weighted number of times the colleague appears as second author on a paper where the star was first author that year Nbcoauth 12 number Number of times the colleague appears as first author on a paper where the star was second author that year Wghtd_Nbcoauth_12 number Weighted number of times the colleague appears as first author on a paper where the star was second author that year Nbcoauth 2M number Number of times the colleague appears as second author on a paper where the star was in the middle not NTL that year Wghtd_Nbcoauth_2M number Weighted numbe
43. rson and appears in the roster 3 The publication citations for each colleague are added to the database either by copying them from another pre harvested database or by retrieving them from PubMed 4 There will be some false or spurious colleagues that were found in step 2 who upon finding their publications don t list the original person as a coauthor Those false colleagues are removed from their colleague lists 5 Reports can be generated for statistical analysis Publication Harvester and Colleague Generator Software Requirements Specification 3 Using the SC Gen software Now that SC Gen has been installed it can be used to generate colleagues Before you can do that you ll need to use the Publication Harvester to create a database Once you have that database SC Gen will search through it generate colleagues and create the reports 3 1 Specify the Roster File The SC Gen software uses a roster file to select potential colleagues To do that it uses a roster file It s a CSV file that can contain a roster of scientists one row per person It can also contain a smaller or different set of people The CSV file contains the following columns e setnb text length 8 identifier for the person e fname text length 20 first name e mname text length 20 middle name e Iname text length 20 last name e match namel text length 20 PubMed formatted name e match name2 text length 20 PubMe
44. social network report section 11 Jan 2008 Andrew Stellman Added Before you generate the social networking report section fixed screenshots SC Gen had a typo in a label 23 Jan 2008 Andrew Stellman Added fault tolerance to the Social Networking report and changed square and regular databases to first degree and second degree 23
45. to serve as a guide to people who want to use the SC Gen software and the Social Networking Report 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 SC Gen software and Social Networking Report software on a machine running Windows XP It covers e Installing the SC Gen software e Preparing the input files e Using SC Gen to generate colleagues from a Publication Harvester database e Using SC Gen to generate reports e Using the Social Networking Report software to generate a social network report from two databases generated by SC Gen 1 3 System Overview The purpose of the SC Gen is to search through a database created by the Publication Harvester project to identify potential colleagues of each star where a colleague is a person who coauthored a particular publication with a star It is then used to gather publications for each colleague and generate reports for analysis of the colleagues in the database The purpose of the Social Networking Report is to search through two databases that were created by SC Gen for the same set of stars The first database called the regular database is used to connect colleagues to their stars to form a first degree social network The second database called the square database is used to connect those stars to other stars they coauthored with
46. y you are acting on behalf of you may not add another but you may replace the old one on explicit permission from the previous publisher that added the old one The author s and publisher s of the Document do not by this License give permission to use their names for publicity for or to assert or imply endorsement of any Modified Version 5 COMBINING DOCUMENTS You may combine the Document with other documents released under this License under the terms defined in section 4 above for modified versions provided that you include in the combination all of the Invariant Sections of all of the original documents unmodified and list them all as Invariant Sections of your combined work in its license notice and that you preserve all their Warranty Disclaimers The combined work need only contain one copy of this License and multiple identical Invariant Sections may be replaced with a single copy If there are multiple Invariant Sections with the same name but different contents make the title of each such section unique by adding at the end of it in parentheses the name of the original author or publisher of that section if known or else a unique number Make the same adjustment to the section titles in the list of Invariant Sections in the license notice of the combined work In the combination you must combine any sections Entitled History in the various original documents forming one section Entitled History likewise combine any sectio
Download Pdf Manuals
Related Search