NeuroScholar Core 1.4 User Manual
Contents
1. In this state the system displays summary information for either the whole system or for a specific KB When you first run the system the first thing you see is shown below E NeuroScholar Knowledge Browser Ja Eg Application Admin Graph Help ae E tosin Password p 4 Knowledge Base Gully Active Knowledge Bases on this system KB Address Model Restore Build Timestamp Gullybrainwalk org neuroscholar v1 core 2005 09 22 09 21 06 0 isullviconnectvitvdb org neurascholar w1 connectivity 2005 06 06 12 31 09 0 isullyvieln org neuroscholar v1 eln 2009 09 20 12 39 17 0 Gullyicn org neuroscholar v1 core 2005 09 18 18 32 28 0 fsullyikhan iO org neuroscholar w1 whole 2005 05 31 03 41 45 0 GulWwneuart org neuroschoalar w1 neuart 0059 08 23 10 56 59 0 Gullynip org neuroscholar v1 core 2005 09 21 18 38 14 0 Gullepubmed100 oarg neuroscholarv1 core 2005 06 07 19 32 39 0 CUllyipubmedso ora neuroscholar 1 core 0059 06 07 19 32 29 0 Gully swanson org neuroscholar w1 whole 2005 08 07 19 31 23 0 fsullviswansonlab org neuroschnolar w1 whole 2005 09 13 15 07 12 0 Gully swansonlab2 org neuroscholar 1 whole 2005 09 05 17 41 11 0 Gullytempo10 org neuroscholar 1 Alp 2005 09 18 19 38 26 0 Gullyivatistab ora neuroscholars1 core 2005 09 16 11 54 50 0 Archived Knowledge Bases Located in CADocuments and Settings Administratonhty DocumentstNeuroscholariaource Eodelcwofarchlwes a File Name Size Bytes connectivityDlatab2. D 5 E iq a Tia bD Interpretation B a aK y a Relation BC o F B F z 5 A Fact C Interpretation C DAA AL OOO Figure 1 the design of the core model in the NeuroScholar system This approach may be generalized to any disparate source of information that could be of interest to the construction of a knowledge representation within neuroscience A very wide range of data is available to neuroscientists from which they construct their understanding of the subject This includes their notebook pages posters at conferences powerpoint presentations images and data files downloaded from the web All of these resources in theory can contribute to their knowledge and all of them could theoretically contribute to the construction of knowledge models This and other functionality has been built into more the more advanced versions of NeuroScholar that have programming structure built on the foundations of the core system 2 What you can do with NeuroScholar Core 1 4 NeuroScholar is primarily a system for managing your own knowledge Most neuroscientists read a very large number of papers on a daily basis NeuroScholar permits users to create a Knowledge Base KB of facts based on the published literature that directly links to the primary literature itself These facts may then be linked together to construct an argument These facts take the form of annotations over the literature using freeform text
3. org neuroscholar vl core 02 resources bibliography Article Resource Publication Article Links ResourceCollection Journal BibliographicFragment Scientist Relations cites As a knowledge management system for the neuroscientific literature the Article view is the mainstay Resource for Meuroscholar Given the massive availability of full text articles to most research institutions we expect that the vast majority of information within the system will be derived from Articles The primary distinguishing feature of this view from Publications are the Citation management tools which help upload data from Publled from EndNote formatted text files startinsert l StartQuery urrent KB Gulkyijen Logged in as root admin Two buttons appear providing additional functionality We will consider the startInsert button later If we click startQuery we enter the Query state 9 1 3 Query When entering the query state you will see a blank form where you may enter criteria for the attributes you wish to search for in the KB You may use the character as a wildcard Some controls such as for Author shown below have pull down boxes that permit multiple criteria to be specified so that the system will search for views that satisfy all criteria Hit the executeQuery button to run the query hit clearQuery to clear the form o NeuroScholar Knowledge Browser JE Appli
4. Single label methods to localize Endocrinology Sarkar Leche This is a very interesting fragment O Zoom Rotate 5 Radius O Hyperbolic Right click nodes and background for m Relation nodes behave in the same way that data nodes do when the user is not logged in When the user is logged in however the user may delete the relation from the viewgraph instance pane 5 5 3 Visibility Controls Nodes may be made temporarily invisible through the controls on the viewgraph panes lt may be required by the user to manipulate the visibility of nodes more directly and by selecting Graph gt View Visibility gt View Definition Visibility or Graph gt View Visibility gt View Instance Visibility the user may load or dismiss views from the view graph currently loaded in memory 5 5 3 1 View Definition Visibility o View Definition Visibility e r 4 KnowledgeStatement amp y Experiment e e Fragment amp r C experiments e je 3 Model e r utilities amp Y A models vj CI fragments amp r CJ labNotebook w CJ bibliography e e 3 LiteratureSearch e je 3 BibliographicFragrnent e je 3 DescriptionFragment amp 3 CitationFragment amp y 3 Article i 9 Journal Z o r 3 interpretationFragrmerdt cos When the View Definition Visibility control is selected a tree with checkboxes on each node opens up The tree corresponds to t
5. NeuroScholar Core 1 4 User Manual Build 1 4 001 Knowledge Mechanics Research Group University of Southern California 2005 Contents NEUROSCHOLAR CORE 1 4 USER MANUAL cccsssssssssrrecssssccccccsssssssssssccccseesessssccccsssssssssscccceseoeees 1 ARO CON Oo 3 2 WHAT YOU CAN DO WITH NEDRO SCHOLAR CORE Topo 4 3 1HE NEURO SCHOLAR LICENSE AAA 5 AOS EM SU ANA AAA 5 4 1 Release O 00L SOME Aaron al LUSTANGIIOW GUO SCIUD POGUINED eiii ikea EEEE EATA shone E A S 2 PAOUR IOURINOUG INES EN a a a E 6 5 1 TES S E e a a E 6 ll AA oa lta otal eat Rel esd deat EEE teats 7 ERRA Docume ano aaa a a E E 9 O E eek Dect tiara fdas eed ca aca 10 O 1 RRO Re est ee Ce vere a RE Re rT eT Ee TT etree 11 l5 TGD IAT aaa a A RER n A SRE A antes dadcadensccantas deat 13 5 1 6 LS E en E ERTEN EON EN N tl E et St eee EEA 14 la E illo ote oorieca 14 32 E E E E IPE E T A AI E E A E E E E T T tan cens 14 ID KODA Drow et TOUTAN LONDRES AAA 15 5 4 EDSON OTITIS tas ra eats suena E ata neti ea E A eed uence 16 q TADO COVIIIGIOS A A ATA A 17 55 1 The Graph Pane Denion Panes da 18 592 The Graph Pamela lasne Dai EE TEA OEREO EEEE NENA 21 IIA Visibility CORTO A Ad AAA 24 BD Oe VIEW o A O ER 24 aa a A NS 25 O PRO Sai dsd dsd dada 26 5 5 4 Andas der the subsenco aia EEEE R 21 5 6 TRE POUONO S EIA AAA EE EAN AAA AAA AA A AAA 28 SEEM ADMINISTRATION OW TOS ASA 30 6 1 CHAINS BMC E E EE S E A A AA A O 30 6 2 VISTO ME DICO IIA AE AAA A A A
6. 7A Cant 1484 The fine structure ofthe latera urrent KB Gulbyicn Not logged in Quu DISPLAY J Comp Neurol 324 743 42 Article Initials Surname INS Canteras Ra Simerly i Lv Swanson hasz Connections of the posterior niga Journal E Comp Heurol Y Yolume 324 Issue Pages 43 79 ere also identified The effera PHAL method appear to follo laterally directed fibers innerva hese fibers reach cortical are small group offibers courses adjacent parts of field CA1 3 molecular layer ofthe medial p amygdala 4 a moderate grou he posterodorsal part of the ibers continue on to end less he amygdala before leaving t 9 the major output ofthe PA ca his pathway massively innervd stria terminalis before enterin massively in the anteroventral entrolateral part of the ventro Abstract The local tab permits the user to browse the immediate neighborhood of a view by first dragging and dropping the current view from the right hand panel to the left This opens up a display where the user may click on folders representing that view s links and relations to other items in the knowledge base The use may then open those items to view In the following example the articles of one of the authors of the paper have been expanded to be viewed E NeuroScholar Knowledge Browser AE Application 000 Graph Help DISPLAY Bl Santatas Sirnerly Swanson 1992 Connections of the posterior nucle J
7. Ghostscript Location Cigsqs8 14bimMoswin320 6x0 Locate GS App Browser Location CiProgram Filesiinternet Explorerliexplore exe Locate Browser App Adobe illustrator Directora CiPrograrm FilesWadobeuiustrator 10 0 3 Locate Adobe lustrator App Current Working Directory dministratorniity DocumentsiHeuroscholaiisource Codeicwd Change current app folder OK Cancel To ensure proper system functionality you need to tell NeuroScholar where it can find the executable files for Ghostscript on Windows this is a file called gswin32c exe on Mac OS X it is usually usr local bin gs for a suitable Internet Browser such as Internet Explorer on a PC or Safari on a Mac This also permits you to define the current working directory s location which is where NeuroScholar will make local copies of PDF files and other required resources such as temporary files and log files 5 A quick tour through the system 5 1 The System States NeuroScholar is essentially a database application that operates on specific views by being in any one of seven states at any time Each view represents a specific class of data object in the system such as a journal article a fragment contained in an article or a statement describing some fact in the system We will walkthrough the simple functionality of the system to illustrate how it is used and to display screenshots illustrating each state of the system 5 1 1 Home
8. This is a simple combo box with four options Select the first Fill in the form using PubMed ESearch EFetch and hit Gol Citation management tools Fill in the form using PubMed Esearch amp EFetch Y Go Fill in the form using PubMed ESearch amp EFetch Use the PubMed website lew PubMed s Disclaimer and Copyright notice Parse citation from file 7 The system will be active for a short while and if the web connection of the computer is functional should return a dialog box of the following form amp Article Robot PubMed Article Webrobot Total 198 records Swanson OA Gowan Whi 1979 The connections ofthe septal region in the rat J Comp Neurol 18641621 55 id pmid 151 176692 Dong Hi Swanson OA 2004 Projections trom bed nuclei ofthe stria terminalis posterior division implications for cerebral hemisphere regulation of defensive and reproductive behaviors J Comp Neurol 4717141 396 433 ld pmid 1 5022261 Scicli AP Petrovich GO Swanson LW Thompson RF 2004 Contextual fear conditioning is associated with lateralized expression of the immediate early gene c fos in the central and basolateral amygqdalar nuclei behav Neurosci 11901 5 14 id prnid 149 97 8 Goto M Swanson OA 2004 Axonal projections from the parasubthalamic nucleus J Comp Neurol 464141561 5607 id prnid 14 755537 Cancel OK st atus 8 Select one of the references and click OK Th
9. ca fa ci Hi O My Magazines 3 ECM_impexp 0g CT My Music 3 ExportFile bcm EA Camtasia Studio C My Notebook CJ Downloads CI My Notes O Life Files C My Pictures EI My eBooks E Meuroscholar ci My Library 3 BCM_ customer log File Name Files of Type All Files Y ea 2 Select the nar file that they wish to restore to the current database and then hit Open 3 The system will then pop up a Build new Knowledge Base dialog box that does not permit the user to define the system s ontology since that is set within the archive Enter the name and confirm your root status by entering the root login and password onto this form Build new Knowledge Base Knowledge Base Details Knowledge hase name Knowledge base namespace MySQL Administration Root Login Root Password Permissions View Indexes View Data Edit Data User m e er Everyone e e E on cana Select appropriate permissions for the system and hit OK A small progress monitor dialog will pop up and when this is complete you should be in the Home state for an your restored KB with the name you entered in the previous step 6 5 Managing Users Once a knowledge base has been built and selected note that the logs contain a complete description of all SQL commands performed on the underlying database it is now possible to define users and knowledge models and then enter real data into the system Not
10. Click commitinsert to upload this relation into the knowledge base 8 13 Inserting unattached Knowledge Statements 1 Load the KB 2 Select KnowledgeStatement from the KB s homepage 3 From the Documentation page click the startInsert button 4 Enter the statement with any required variable names and values 5 Click the commitinsert button to upload this statement to the knowledge base 9 Additional Support The NeuroScholar project page on Sourceforgeprovides access to the developers in the system If you encounter problems please let us know by submitting a bug report or email us http www sourceforge net projects neuroscholar
11. in as root admin Whenever a view instance is loaded in the Display state in the view panel a Right click nodes an node corresponding to it is loaded in the instance pane All of the node s visible neighbors will also be displayed in the pane The act of double clicking a node will bring it to the center of the graph and load all of its neighbors links and relations and will also load it for viewing in the right hand panel Thus it is easy to navigate the contents of the knowledge base by simply double clicking nodes and traversing the relations that appear As with the viewgraph definition pane the user may interact with the graph by right clicking nodes edges and the background Right clicking the background produces exactly the same effect here as in the viewgraph definition pane and will not be covered again here View instance nodes appear as shown in the screen shot above This depicts an Article view instance where the node s label is longer than one line and so is truncated until the user passes their mouse over the label where it expands to display itself fully As before the functions available to users from right clicking nodes depends on the type of node and the login status of the user As before if the user has not logged in all options available here are simply display functions The user may view the contents of the view itself by selecting Display this View Instance or he she may list any v
12. involved in pain modulation NEUROSCIENCE 70 449 460 id local 5218 Daftar 55 Boudaba E Szabo K Tasker JG 1998 Noradrenergic excitation o magnocellular neurons in the rat hypothalamic paraventricular nucleus via intranuclear glutamatergic circuits JMeuroasci 18 10619 10628 id local 708 Daftary 55 Boudaba Tasker JG 2000 Noradrenergic regulation of parrocellular neurons in the rat hypothalamic paraventricular nucleus Menrascience SOON 9441 743 GA TA id lacal 8 4 Add a PDF file to the reference 1 Start by inserting an article reference from PubMed as described in the How To described above 2 Before inserting the article into the KB examine the entry for the Full Text URL If an entry exists there click the Open Link button URL yl y Full Text URL 1 y dx doi org 10 1016 neulet 2005 06 086 Open link If no entry exists there select Use the PubMed website Citation management tools Fill in the form using PubMed ESearch amp EFetch Y Go Fill in the form using PubMed ESearch amp EFetch Use the PubMed website lew PubMed s Disclaimer and Copyright notice Parse citation from file Both options will open a web browser at a place where it should be relatively straightforward to navigate to the full text article Save this article to your hard disk in a known location 3 Click the Import button of the Full Text File control This wil
13. isomers showed a significant effect on ton stro pic Ni IDA RA pa er han nd ACP T M 79 was found bo be a gener a mpetitive antagonist for metabo oe eptors imbilulks and exhibited as siuh ar al finity for m lukl a Ka 1153 2 a boi Kn BB 21 eM and mG alule ha Ry ix 94M the ri Lt sente atiy E oe embers of group 1 Mara i I mGluRs re ape ctively Twi athe fF isomers ACPT I 18 and 141 435 ASI ACPT IN 20 wi Piola aisis at thk mma TH eptor miiluk4a i EC a 1242 3 m a 2 0M and ci nee tit ly an ta igonists with low al ffin ity for mGluRla and mGluR Ky gt 300 ut Fin ally q HAR IR LEFT lo 20 was a compe itive aniagonist wil th poor bul significant e iniy for mislult4da Ke 220 u M ne se results demonstrate that the addition of u third e xy lic gr wip te pi can c hange its actiy ity from agonist to anta nist and either increase or decrease 113 ivi andor affin nity for the various mGluR smile clearlnsertForm commitinsert Plugin urrent KB Gulky wattsiab Logged in as root admin 4 You can select text as shown above to delineate a passage of interest The blue points of the yellow polygon control the size of the most outward points of the polygon The green points move inside the polygon allowing you to indent the shape to perfectly fit a small paragraph or sentence of text 5 You may add multiple excerpts 6 Drag and drop the excerpts to move them around the document 7 Right click an e
14. looks like this E 3 The dialog box used to enter variables is shown below and is essentially a spreadsheet where you may list variable names such as concentration or some other data variable the value and the units used When entering these values you should try to be consistent between different fragments in terms of how you name variables Attach Generic Data Data Attributes Variable Variable name data value units used 4 Hit the commitinsert button to upload this fragment into the KB 8 9 Display a fragment As with the How To concerned with locating an Article the easiest way to display a fragment is to run a query 1 2 Load the Knowledge Base Click BibliographicFragment Click the startQuery button Enter some selective criteria on the form Click the executeQuery button Locate the desired fragment in the list and click the selectForDisplay button to display the reference 6a If you can t find the correct fragment in the list scroll down to the end and look for more pages 6b If you still can t find the fragment hit the back button in the toolbar and change your query criteria 1 8 10 Delete a fragment Use the How To above to display the fragment you want to remove 2 Click the deleteView button 8 11 Delete an article with all contained fragments 1 Use the How To above to display the fragment you want to
15. to perform the essential parsing and rendering of the PDF file 1 Start by either inserting an article with a PDF file or query the KB to show a specific Article 2 Select BibliographicFragment from the Insert pull down control at the bottom of the form sert Dependents Relations sert Dependents Relatons BibliographicFragment Fragment cites Publication 3 The system loads the file and then presents the user with the following screen amp NeuroScholar Knowledge Browser ay La x Application Admin 1200 Help gt E E Login root Password perreo Fl ix Knowledge Base Gullyiwattslab INSERT Type 3 Name OO CHAR T Med Chem 1997 40 3119 3125 Synthesis and Pharmacological Characterization of Aminocyclopentanetricarboxylic Acids New Tools to Discriminate between Metabotropic Glutamate Receptor Subtypes eign C Acher Fr d rique J Tellier Robert Azerad Isabelle N Brabet Laurent Fagni and arPhilipp R Pint rp oe irre E Chera a Pharmacoleigues el Terdiooloripres URA a ONES Urns Reni deceo Pola Y ipis Peres 7 rO Parris Ci aler 06 France oral Ca iri INSERM CNRS de Plarrr epee Ar Endocrinalos UPR a02 lt 9 rrit ado la Corckmille 34094 Mi antler Cooder 5 Frane Receined Alarch 27 14977 tercoisomers of aminocyclopentane 1 3 A loca ec dnd acid ACPT 1 18 and a9 I ERL ii r20 a 3S 45F 111 fad gs been kynthesiond and evaluated for
16. Come Neurol 5247402 Co Scientist Article Po LW Swanson er ConterencePresentation ENI NE Cantera sites a Book bese pS e IRB Simerly id ublication f 1008 Ly Swans onia a BookChapter a be Resource 1992 a Thesis CJ Article B Saper E Swan Journal E Comp Neural Y 2 NS Canteras 2 RB Simerly EJ Journal Issue ee Sone ion Pages hara i BibliographicFragment a aT 3 FesourceCcollection ere also identified The effere cites PHAL method appear to follo laterally directed fibers innera hese fibers reach cortical are small group offibers courses adjacent parts offield CA1 3 molecular layer of the medial p amygdala 4 a moderate grou he posterodorsal part ofthe ibers continue on to end less he amygdala before leaving t 9 the major output ofthe PA ca his pathway massively inner stria terminalis before enterin massively in the anteroventral entrolateral part of the ventro Initials Surname Connections ofthe posterior niga Yolume Abstract Current KB Gulkyjcn Not logged in 6 System Administration How tos The NeuroScholar system is built on an underlying MySQL database and the user may manipulate the database through MySQL This involves the creation destruction saving and restoration of knowledge bases To perform these functions the user must login as root on the browser itself to activate the Admin menu 6 1 Creating a new knowledge ba
17. Toolbar commands The vast majority of computer users today are web users and we have designed the NeuroScholar user interface to provide basic web like navigational capabilities The toolbar has a back button a forward button and a button for home This permits users to go back to previous states of the system and then advance forward to subsequent states The home button resets the current KB and returns them to the home state displaying counts of all views in the system 5 4 History commands The toolbar also contains a toggle button that permits the user to see their history This is shown below The user may click on any of the history items listed to return to that item If the user then does something in the system ofher than perform another history based action then that action will become the next item in the history list and all subsequent history items will be removed The history pane can be removed by clicking on the History toggle button a second time Application Admin Granh Help Knowledge Base Gullyjen zil Clear History Gultyjcn html Article anuai Canteras Simerly Swanson 1992 Connecti GullyicnistartqueryiArticle eee Comp Neurol 324 743 79 a IGulkyjcniexecuteQueryiiewType Article Scien Article Guy jcnidisplayView Article UID 44057 Initials Surname Canteras IL Swa nson Year 1907 Connections oft
18. a field CA Other seemingly minor inputs including cholinergic fibers from the substantia innominata dopaminergic fibers from the ventral tegmental arca and serotoninergic fibers from the dorsal nucleus of the raphe were also identified The efferent projections of the PA as determined with the PHAL method appear to follow five major routes 1 a relatively small group of laterally directed fibers tnnervates the dorsal endopiriform oucleus and a few of these fibers ranch cortical aren TR ond the lateral entorhinal area 2 another amall group of fibers courses medially to innervate the ventral subiculum und adjacent parte of field CA 3 many fibers course ventrally to innervate the outer molecular layer of the medial part of the posterior cortical nucleus of the amygdala 4 n moderate group of fibers courses rostrally to innervate primarily the posterodorsal part of the medial nucteus of the amygdala although some fibers continue on to ond less densely in rostral parts of the medial nucleus of the amygdala before leaving the amygdala through the anan peduncularis and 5 the major output of the PA courses through the stria terminalis One branch of this pathway rua innervates the of shunt nucleus af the bed nuclei of the stria a terminalis before mw 4 pr of 37 pages E ih Mel TE a clearinsertForm commitinsert Plugin Current KB Gullyjicn Logged in as root admin V4 BAVA VA VA A 5 3 Knowledge Browser
19. amyqdala J Comp Neurol 324 143 79 ViewTable_id 44057 locked OA Swanson g thumbnail machinelndex Canteras 1992 324 143hidelpmid 1430327 urrent KB Gully cn Not logged in 5 6 Tree commands The user may view the contents of the KB as a tree by selecting the Tree toggle button from the Toolbar shown as This opens the tree panel on the left hand side This panel has two tabs global and local The global tab is simply a shallow tree representing the entire contents of the knowledge base organized by package and view type shown below l amp NeuroScholar Knowledge Browser Application du Graph Help A Sullyicn CJ core CJ 01_knowledge 702 resources Q ES 02 resources bibliography ConterenceProceedings 0 Y Book 10 ConterencePresentation 0 article 11967 Q ig Aas Ozol Aas L Auber a AUbe Berk b Berk Brook EJ Broo Cani E Brooks Brow E Brown Brunke E Bruns Bucht Y Buck Bullie Y Bullie Burd a Burette Burrill Burris Burton 3 Burwe Byers E Bryers B url 3 B ur Calc Calced Calton E Calupe Gaming tammer Carmo Q Canoa Card ae Canonaco Tavolaro Facciolo 1997 Dime Fa Canosa Cerda Reverter Peter 2004 Bra
20. aseDdod0o05 nar ofa fos cn zip 13411254 icni zip 13260043 Complhieurol zip 131564530 Comprhieuroll zip 1393995088 urrent KB Gully Not logged in Each of the links in the top half of the screen represents a different KB with the type of model supporting its construction and the date of its creation listed Note that there are many types of model this manual is only concerned with those of type org neuroscholar v1 core representing the core functionality of the system The bottom half of the screen contains NeuroScholar archive files that contain all the data from a specific knowledge model A user may restore the data from one of these archives by clicking on the link to the file If a user selects one of the KBs on the system he she is taken to the following screen amp NeuroScholar Knowledge Browser uE Application cd Granh Help gt ea Login Password F K KnowledgeBase Gulyien III Knowledge Base jen org neuroscholar v1 core Package View Refation Parents View Count knowledge KnowledgeStatement contradicts ISabout SUBIDOS resources Publication Resource Resource Resourcecollection Scientist resources bibliography Article Publication Resource Book Publication Resource Bookchapter Publication Resource ConferencePresentation Publication Resource ConferenceProceedings Journal Thesis Publication Resource 0 fragments BibliographicFragment Fragment KnowledgeStatement 0 Fragm
21. cation Admin oro Help i Login root Password sevens p i Knowledge Base Gullyjen y QUERY ML ARAS Initials Surname Author 2 x 17 swanson INS Canteras do ke Es kefu Anfu ints befe ba Year ip alin a ig a ig ey eg aig Tag Taig Tg Tg Dag De De Te sit oe Journal Volume Issue Pages Lippi 7 f l eke fs pd AAA AAA AAA Abstract clearQuery executeQuery urrent KB Gulkyjen Logged in as root admin 5 1 4 List Upon execution of the query the system will list all entries in the system that satisfy the stipulated criteria In our example seven articles were found These records are listed in order of their indexes which correspond in this case to a citation that you might find in a reference If more than 100 records are returned they are split into pages where the user may click a link at the bottom of the list to view the next 100 The user may select a specific view and then hit displayView to move to the next state Es NeuroScholar Knowledge Browser aota Application Admin oro Help Ex Login root Password sevens p i LIST a Lanteras simerly swanson 1992 Connections of the posterior nucleus of the amygdala J Comp Neurol 324 143 79 Canteras Simerly Swanson 1992 Projections of the ventral premarimillary nucleus J Comp Neurol 324 199 212 Canteras Simerly Swanson 1994 Organization of projec
22. cosa 31 6 3 VIBE SA IL A E EE A A E AE O E 31 6 4 OSO FAEAE SADO ANOTA AAA SAA AS SAA A SARA 32 6 5 a II A pees turtle E aie es terse tan varus vaieseag usu eoaeeius EA OT ENE ease 34 HE COURTS SV SATIVA A o 35 Pd VA A att 35 LOW TOS NON 35 3 1 Enler a hiokooraphie Terence mio IDO SNS USE LAO teed ioosansawesouba vasseessawnseebat 36 8 2 Orati ze DADES USI d ROS OnT COMO A ads 37 8 2 Upload a library of citations from an EndNote Reference Manager or Procite librar acce 40 8 4 Adda POFO LBC 1 VINEETA A ENN E AA A 42 8 5 Torte A RI co sd ak hat a canal digest cin we ea ceca anu tea dete ciens 42 8 6 PNL TIIE SN lista 43 8 7 TaT a TAON DU ANN OLONE E os 45 8 8 VERTE ET E I E EEA E E A E T ET A E A 46 8 9 D E O L IE EE ANA AA A N E 47 SO LIAT T A ERE E T EE ET E alae htanetia Ds acrensatnate 47 8 11 B E E AED ELIAS as 48 8 12 Linkin UD ITASIMERISIDIDO SUPPOTIS y OF TONNAS TEIGUZONS it 48 Slo TOSCO TRATA RODA S TUIS EE ein 49 IO O O A A ee A Se er Ren Se S 49 1 Introduction The discipline of neuroinformatics can be thought of as the information science infrastructure of neuroscience Ascoli et al 2003 This usually involves the development of new software and databases to manage and publish neuroscientific data Neuroscience already has a robust existing information science infrastructure the neuroscientific literature It has been argued that science may be thought of as a process of inscription meaning that the
23. database 5 The dialog will remain open So you may repeat the process as necessary 6 3 Saving a knowledge base Saving an existing knowledge base to a nar NeuroScholar Archive file is a particularly useful activity permitting data migration between systems and even knowledge sharing between people 1 Select Admin gt Save Knowledge Base 2 Use the login dialog box to confirm your root status on the system System Administator Knowledge Base Login BILLYOCCAM stress Login ro ot Password freer om coca 3 A SaveAs dialog box appears Enter the name and location of where you would like to put your nar file Es Save Save In i My Documents ca fa Ci EE i My Magazines 3 BCM_impexp log CJ My Music i ExportFile bcm CJ Camtasia Studio CI My Notebook EA Downloads C My Notes E Life Files J My Pictures C My eBooks C Neuroscholar Es My Library E ECM_customer log File Name Files of Type All Files Y cae canal 4 When ready hit Save 5 NeuroScholar will dump the entire contents of the current knowledge base to disk as that file 6 4 Restoring a saved knowledge base After saving the data in a knowledge base to a file you might want to restore that knowledge to another knowledge base 1 Select Admin gt Restore Knowledge Base from Archive An Open dialog box pops up amp Open Look In i My Documents x
24. e system will load all the reference information into the form 9 Click the commitinsert button to enter this reference into the knowledge base The view will change into the Display state with grey letters 8 2 Organize papers using a ResourceCollection A ResourceCollection view can permit users to organize their resources according to any criteria You could put all references pertaining to a specific topic in a collection and then create another collection for another topic Unlike directories on your hard drive a single paper can happily co exist in two collections with no difficulty 1 Load the required knowledge base 2 Login to the knowledge base either as root or as a user you have already created in the system 3 Select ResourceCollection from the list of Views to view the Documentation for these views 4 Click the startInsert button You will see a form with the following design Name Description Resources q as Te e Citation management tools Parse citation from file A Go 5 Pick a name for your collection connectivity studies Norepinephrine injection studies or Papers by my boss are all perfectly valid collections to use 6 Enter a short description of the criteria that specify why you are putting these papers into this collection 7 Using the pull down next to Resources select the number of resources you want to include This c
25. e that this step may be omitted with a knowledge base that has been restored from an archive since that system will already have well established preliminary data To insert a new user select Admin gt Add New User from the menu This loads a form where you can insert data describing a new user in the usual way Note that the initial text of the password is masked by ten characters Simply fill in the form and hit commitinsert Once that is complete you may login as this user from the browser To list display and edit the users in the system select Admin gt List Users from the menu This lists all the users registered for this knowledge base in the system You may select one to display it and then edit their details if required 7 The core system The core system of NeuroScholar handles the lowest level of functionality downloading articles and other bibliographic resources whilst permitting the user to build a repository of knowledge statements based on those resources 7 1 System packages The system has a modular design based on series of packages This design allows us to construct versatile knowledge bases tailored to different knowledge management tasks but for now we restrict our attention to the simplest aspects of managing information in the published literature Basically the views have been organized according to the following packages e Knowledge views in this package are c
26. ent KnowledgeStatement 0 Ges O urrent KB Gulkyjen Hot logged in This screen lists all the different views and available relations in the selected knowledge base with counts of the number of instances of these views Notice that the system comes preloaded with 18654 instances of the Journal view taken from PubMed s online database of journals The KB displayed here is a restored version of the CompNeurol 1970 2005 nar NeuroScholar archive file that is distributed with the NeuroScholar Core 1 4 system This knowledge base contains citation information from every issue of the Journal of Comparative Neurology from 1970 to 2005 in our attempt to make a definitive knowledge model of the literature underlying tract tracing experiments For this purposes of this distribution it serves as an excellent example for new users of the system If the user clicks on any of the names of a View such as Article for example they will be taken to the documentation state 5 1 2 Documentation In this state the system displays some documentation describing the view This documentation describes any Parent views of the view in question as well as links dependencies and children where necessary Clicking on links permits the user to easily navigate to those views documentation as well Ey NeuroScholar Knowledge Browser Ja Eg Application Admin oro Help ea Login root Password evens p i DOCUMENTATION
27. fundamental process of performing scientific work is simply that of generating inscriptions and then transforming those inscriptions from one form to another according to carefully defined rules Latour and Woolgar 1978 If this is the case then the literature is the ultimate end product of most scientific work it is the repository into which the majority of scientific knowledge is deposited it is the currency through which scientific value is judged and it is also the crucible in which discoveries and contradictions are formally aired and elucidated For this reason the neuroscientific literature is the primary target for the action of the NeuroScholar system The basic schematic organization of the NeuroScholar system is shown in Figure 1 Quite simply the literature exists as a large number of disparate scattered portable document format PDF files that may be referenced via a set of uniquely definable keys from online sources such as PubMed or each documents DOI address NeuroScholar users may delineate fragments form within these publications to form individual facts Once this step has been completed users may then compile fragments together to support interpretations and then may build relations between those interpretations When applied to specific typed data in a well defined ontology this schema defines the basic design of the NeuroScholar system D DD po E S H Ge Interpretation A a pa am _ E
28. he Radius control allows you to manipulate the extent of the graph that appears relative to the central node of the graph You can expand the radius to show every node or you can shrink it to show only the central node with none of its immediate neighbors The Hyperbolic control permits the extent of apparent lensing within the panel This causes nodes in center of the panel to lie further apart than nodes at the panels edges 5 5 2 The Graph Panel Instance Pane amp NeuroScholar Knowledge Browser Ji Eg Application Admin Graph Help KE Login root Password sevens i Instance DOCUMENTATION org neuroscholar vl core 02 resour Publication Resource Publication Children Thesis BookChapter Book Conference Links Scientist ResourceCollection Bibhographi Canteras Simerly Swanson 1992 Relations cites Connections of the posterior nucleus of the amygdala J Comp Neurol Sag 143 79 A Publication is a Resource that has been pub restrictions will typically exist for Publications work are publications and so the importance of E This view has five children Articles Books Be If the user wishes to keep track of other types of and other documents he she should use the Pub If the user wishes to derive Fragmenta from this Publication as a POF file with the Import fort ID control and Keywords may also be tracked MA Cd Teena Startinsert star Query urrent KB Gulkjen Logged
29. he data in that form the Plugin toggle button permits them to flip between the text based data as shown in the previous section and the more elegant plugin view shown below Application Admin Graph Help E El e INSERT we e ma THE JOURNAL OF COMPARATIVE NEUROLOGY 324 143 179 1992 Connections of the Posterior Nucleus of the Amygdala N S CANTERAS RBD SIMERLY ann LW SWANSON Department of Biological Sciences University of Souther Calitornia Los Angeles California 0059 2520 ABSTRACT The connections of a relatively homogeneous band of neurons in the caudal amygdala have been examined with anterogrede and retrograde soonal tracing methods in the rat This region called here the posterior nuclens of the amygdala PAL corresponds in pert to an area that has boca referred to as the cortico amygdalod transition area posterior part of the medial nucleus of the amygdala amygdalo hippocampal transition area and posteromedial basal nucleus Experiments with fluorogold and phaseolos vulgaris leucongghutinin PHAL indicate that the major neuronal input to the PA arises in the ventral premammillary nucleus and that substantial projections also arise in olfactory related areas such as the medial nucleus of the amygdala bed nucleus of the accessory olfactory tract and posterior cortical nucleus of the amygdala as well as in the ventral subiculum and adjacent parts of in derm
30. he hierarchical package design of the UML model that underlies the system and so a good understanding of the data model being used in the system is required In the tree each folder contains a number of views and if the user unchecks a folder all contained views within the folder will be unchecked as well Each document icon within the tree corresponds to a View Definition and if these are unchecked they effectively disappear from the data model i e they are removed from the viewgraph definition pane and any of their instances are removed from the viewgraph instance pane 5 5 3 2 View Instance Visibility s View Instance Visibility amp CJ experiments amp Y Model amp J utilities amp C models CJ fragments amp C labNotebook O bibliography e Y LiteratureSearch E E BibliographicFracrmert E E DescriptionFragment CitationFragrnent e Article Bito Dec oa 1 y Bito Deisseroth Tsien 1995 O Blume Seifert Lebrun Malle O C4 Coogan Figgins 2003 Cir O Daniels Patten Roth Yee Fl E m ee i Similar to the View Definition Visibility control the View Instance Visibility control opens a tree based on the hierarchical package design of the UML model that underlies the system In this tree the folders and views do not have checkboxes The user may open up a specific view and alphabetically browse the contents of the knowledge base Each view insta
31. he posterior nucleus ofthe amygdala i Title Journal E Comp Neural Y Wolume 324 Issue 2 Pages 1 43 75 ere also identified The efferent projections ofthe PA 4 PHAL method appear to follow five major routes 1 a re laterally directed fibers innervates the dorsal endopirifo hese fibers reach cortical area TR and the lateral ento small group offibers courses medially to innervate the adjacent parts of field CA1 3 many fibers course ventr molecular layer of the medial part ofthe posterior cortic amygdala 4 a moderate group of fibers courses rostra he posterodorsal part of the medial nucleus ofthe am fibers continue on to end less densely in rostral parts a ie enone before eels the Pees nuar the E edites F deleteView _insertanother Insert urrent KB Guilyjicn Logged in as root admin Abstract 5 5 Graph commands NeuroScholar is based on the design of a network of nodes and edges a graph and it is possible to view both the definition of the data model and the data itself according to that design To activate the graph pane click the graph button in the tool bar ica This also activates the Graph menu Gg a o o E Application Admin tesa Help Definition Instance DISPLAY Resource any Canteras simeny awanson 7992 Connecti Publication y Comp Neuro 324 743 79 Article Initials Surname Canteras contradicts RB vw Swanson isan Co
32. iews linked or related to the clicked view by selecting List Linked view instance gt In this case another menu of all the possible types of view pops up so that the user may select the required list This executes a list command on the system and displays the data in the right hand panel If the user has logged in a far larger number of options are available The user may insert an instance of a specified view definition thus permitting BibliographicFragment instances to be inserted from a given Article instance lf the user selects Opinion from the popup menu a small box with five stars appears displaying the user s opinion of how reliable the data represented in this instance is On clicking the Insert Relation menu item the system will pop up a list of possible relations that may be inserted If the user selects one of these the system will pop up a new frame with a version of the view instance graph that is currently in memory currently centered on the node being right clicked on Each node in the graph that is eligible to be the recipient of the relation appears in green After identifying the target for the relation right click the target and select Insert Relationship from the pop up menu The system will then insert the appropriate relation into the graph This feature is somewhat cumbersome and may be dropped from future versions of the system amp pCREB Optimization Comments supports
33. irm the addition of this ResourceCollection to your KB click on commitinsert The system will insert the view and revert to Display mode An example of a small ResourceCollection is shown with links in the view instance graph 8 3 Upload a library of citations from an EndNote Reference Manager or Procite library Users may have large existing libraries of references that they do not want to have to go through individually uploading references into NeuroScholar We permit these references to be uploaded as a batch file You will need a copy of EndNote to perform this task 1 Repeat the steps required to insert a new ResourceCollection load the required knowledge base Login to the knowledge base either as root or as a user you have already created in the system Select ResourceCollection from the list of Views to view the Documentation for these views Click the startinsert button At this point if your database is based on Reference Manager or ProCite convert it to EndNote using the mechanisms within the reference management software Open the file in EndNote and export it to a file using EndNote s File gt Export function Select the option Parse citation from file shown below from the Citation Management control Citation management tools Parse citation from file we Go Parse citation from file Use the PubMed website 8 lew PubMed s Disc
34. l open a File Open Dialogue box Locate the PDF file that you have just downloaded This will rename the file and upload it to the local directory in your system The file naming scheme is dependent on the type of reference but for Articles it is based on the name of the first author the year the volume number and the start page Full Text File swanson 2005 387 80 pdf Import VIEW Clear At this point the PDF is now loaded into the system 8 5 Locate an Article in the system The system offers several ways to find specific views in the system The easiest way is to run a query 1 Load the Knowledge Base 2 Click Article 3 Click the startQuery button 4 Enter some selective criteria on the form 5 Click the executeQuery button 6 Locate the desired article in the list and click the selectForDisplay button to display the reference 6a If you can t find the reference in the list scroll down to the end and look for more pages 6b If you still can t find the reference hit the back button in the toolbar and change your query criteria 8 6 Fragment a PDF file The primary functionality of this core release of the software is to permit users to build a repository of searchable fragments derived from published papers Thus inserting fragments derived from PDF files is essential for this process Note that this section of the system uses the Multivalent java library
35. laimer and Copyright notice An file open dialog then opens Select the file of interest and click Open lo Downloaded File Location Lookin CSmblograsty ala Y Ref Database 3 28 txt Y Ref Database 3 28_temp txt 4 temo txt Y J_Medline txt Y Ref Database 3 28 ENL Y Ref Database 3 28 pdt Y Ref Database 3 28 pdx File Name Files of Type All Files y Loa 9 A progress dialog will open as NeuroScholar parses the file amp Progress 1076 Articles parsed PONS EE _ a With a particularly large database this may overload the system If this is the case click Cancel The system will continue the next step and the remaining text in the reference file will be saved to disk by adding temp txt to the file name 10 In e ther case the system will display the following panel You may select multiple entries for all the citations you wish to load and click Ok The system will then insert all selected references into the knowledge base amp Article Robot PubMed Article Webrobot local 6884 Dacosta APC Kampa RJ Windle AJ Ingram CD Lightman SL 1997 Region specific immediate early gene expression following the administratio of corticotropin releasinda hormone in virgin and lactating rats Brain Research 270 0191 162 id local 5874 Datny N Dong VG Prieto Gomez C Reyes Vazquez C Stanford J Qiao JT 1996 Lateral hypothalamus site
36. ll be taken to the edit state see below If the user clicks the deleteView button he she will delete the view along with any other views that are dependent on it before being returned to the documentation state for this view definition If the user clicks the insertAnother button he she will be taken to a blank insert form for this view see below A pull down box permits the user to insert dependent views such as a Bibliographic Fragment from an Article or relations such as a cites relation 5 1 6 Insert If the user is logged in he she may insert a new view In this case the user is presented with a blank form where he she may enter data and when completed hit the commitinsert button at the bottom of the view panel to finalize the insertion into the database 9 1 7 Edit If the user is logged in he she may edit existing views In this case the user is presented with the same form as shown in the display view but all fields become active and editable The user simply makes changes as required and then hits commitEdit to upload those changes to the knowledge base If the user wishes not to commit those changes hitting cancelEdit will return them to the previous display state 5 2 Plugins Specialized plugins such as the Fragmenter shown below permit the users far more complex control over their data than a simple textual form However if the user wishes to view t
37. nce will have checkbox which will load it and its immediate neighbors into the view instance panel This is a useful feature to permit the user to load specific views into the viewgraph instance pane quickly 5 5 3 3 Profiles These are predefined visibility controls for a collection of view definitions Select Graph gt Profiles gt and a list of profiles will come up With a large complex model this permits the user to concentrate only on a specific subtask 5 5 4 An aside the substructure of a view Each view has a graph like substructure that may be accessible for viewing by selecting Views gt Show View Substructure The view panel shows all primitives for the current view with all data in a generic form lt is possible to look at any of the data in the other primitives simply by right clicking the primitive and selecting Show this primitive from the popup menu E NeuroScholar Knowledge Browser l cog Application ooo Graph Help K Login Password ig i Knowledge Base Guilyjcn DISPLAY sey Keyword 5 Spurn word 7 E ey lacey aor keyword 4 po acora d Resource o g IW NS URIO g Scientist keywora E y Keyword 10 J Come Neurol S24 745 79 Volume 324 Issue E Canteras Simerly Swanson 1992 journal_id 4668 ViewTable_id 44057 namespace timestamp 200506805011852 Canteras Simerly Swanson 199 Connections oft indexString j
38. nnections ofthe posterior nucleus ofthe amygdala Ea Journal E Comp Neurol Ml Volume 37 Issue 2 Pages 1143 75 were also identified The efferent projections ofthe PA a PHAL method appear to follow five major routes 1 are laterally directed fibers innervates the dorsal endopirifog hese fibers reach cortical area TR and the lateral entor small group offibers courses medially to innervate the adjacent parts offield 641 3 many fibers course ventr molecular layer ofthe medial part ofthe posterior cortic amygdala 4 a moderate group of fibers courses rostra he posterodorsal part ofthe medial nucleus of the amy fibers continue onto end less densely in rostral parts a ne amy ee before le Nps ann rgdala through the editview deleteView A insertAnother Insert Abstract urrent KB Gullyjcn Logged in as root admin The Graph panel has two tabs Definition and Instance 5 5 1 The Graph Panel Definition Pane This pane shows the design of the knowledge base that is currently loaded It may be quite complex and is based on a visual notation called the Unified Modeling Language which is widely used in the computer industrial to describe data schemata Essentially the design shows the organization of view definitions in the system and their possible interrelationships You may interact with this representation by left or right clicking on the nodes the edges or the background Note Mac OS X
39. ollow the steps in the How To called Fragment a PDF file 2 After selecting a polygon right click the yellow excerpt Select Annotate and then either Text or Voice 3a The text annotation dialog has a space in which you can enter free text and you can select where you d like the annotation to appear on the page These options include None to keep the annotation hidden Center to place the annotation inside the excerpt delineation or compass points to place the annotation outside the delineation at the appropriate place O None Center North gt South East O West oe eo 3b The voice annotation dialog is a recorder box Hit the record button and speak A line will appear in the black region to show a sound trace When you are finished click stop and Submit Voice Annotation Editor Up to 60 se Ready Length 0 0 Position 0 0 EUA cancel 4 If you wanted to make an annotation on an excerpt act as the Knowledge Statement of this fragment right click the excerpt in question select Annotate and then Set as Knowledge Statement The annotation will then be underlined if it is displayed on the page 8 8 Insert a fragment with data annotations 1 Follow the steps in the How To called Fragment a PDF file 2 After selecting a polygon click the Attach Data to Fragment button on the tool bar of the fragmenter plugin This button
40. oncerned with statements of Knowledge and their relationships e Resources views in this package are concerned with external items that contain knowledge In this system these are publications which might be articles books etc e Fragments views in this package are concerned with excerpts taken from the resources each of which forms a small specialized knowledge statement called a fragment These fragments are literally annotated excerpts taken from PDF documents within the users document library 8 How tos To make this section oriented towards helping users accomplish specific tasks we have listed a number of unitary tasks with a complete description of how to accomplish that task 8 1 Enter a bibliographic reference into the system using PubMed 1 Load the required knowledge base 2 Login to the knowledge base either as root or as a user you have already created in the system 3 Select Article from the list of Views to view the Documentation for Article views 4 Click the startInsert button 5 If you know the citation details of the paper you are interested in enter a few details of the reference into the form The best approach is to enter the last name of the first author the year the volume and the page of the start of the article This always returns a unique reference If you do not know these details enter what you do know and continue 6 Use the Citation management tools form control
41. ould be arbitrarily high see below Name Description Resource Resources i Y a Eh management tools e Citation from file 8 In each box of this list type the wildcard character followed by the name of one of the authors or a distinctive word from the title Note that the paper you want to add to the ResourceCollection must already exist in the database 9 The lookup box will return a list of entries select the desired citation and move to the next one y NeuroScholar Knowledge Browser Ax Application Admin Graph Help DISPLAY Newton s hypothalamic papers A Hame Newton s hypothalamic papers Canteras Swanson Simerly A os Newton Canteras papers about Hypoti Description Resource as Swanson Risold 1994 Canteras Swanson 1992 The dors ee octy Proc H i q lie a body Proc Natl Acad Sci U S A 89 10 ni SR ERS pee ACS Canteras Swanson Risold 1994 0 YP pap Resources Phaseolus vulgaris leucoagglutinin Canteras Swanson 1992 The Canteras Swanson Simerk 1992 Canteras Swanson Simerly 1994 hypothalamus a Phaseolus vulgaris Citation management tools Canteras Swanson Simerly 1994 Use the PubMed website Linked Views Article Relations Zoom O Rotate Radius Hyperbolic Right click nodes a Current KB Gulky swansonlab Logged i as root admin 10 To conf
42. pear to follow five major routes 1 a relatively small group of laterally directed fibers innervates the dorsal endopiriform nucleus and a few of hese fibers reach cortical area TR and the lateral entorhinal area 2 another small group offibers courses medially to innervate the ventral subiculum and adjacent parts of field CAT 3 many fibers course ventrally to innervate the outer molecular layer of the medial part of the posterior cortical nucleus ofthe amygdala 44 a moderate group offibers courses rostrally to innervate primarily he posterodorsal part ofthe medial nucleus ofthe amygdala although some ibers continue onto end less densely in rostral parts of the medial nucleus of he amygdala before leaving the amygdala through the ansa peduncularis and Es the major output ofthe PA courses through the stria terminalis One branch of i his pathway massively innervates the principal nucleus ofthe bed nuclei ofthe siria terminalis before entering the medial Anas ia mus ee tends editview editview delete View insertanother _ insertanother Insert sert Dependents Relations Current KB Gullyjcn Logged in as root admin Abstract BibliographicFragment Fragment cites Publication Note that individual controls may have quite complex functionality depending on the view type If the user is logged in several buttons appear at the bottom of the view panel If the user clicks the editVlew button the user wi
43. remove 2 Click the deleteView button 3 If there are fragments associated with this paper then the following dialog will appear Confirm Delete of Dependent Views i You are deleting ARTICLE Acher Tellier Azerad Brabet Fagni Pin 1997 Synthesis and pharmacological characterization of aminocyclopentanetricarboxylic acids new tools to discriminate between metabotropic glutamate receptor subtypes J Med Chem 40 3119 29 The system contains 3 views that are also dependent on this view BibfographicFragmentd f you proceed with the deletion we will attempt to delete these views as well If they also have dependencies the deletion will fail To delete everything click the Proceed with Deletion button 8 12 Linking up fragments with supports or contradicts relations An important function of this system is to permit users to construct an argument from fragments derived from the primary literature You can do this in several ways 1 Load the KB 2 Select either supports isabout or contradicts from the KB s homepage 3 From the Documentation page click the startInsert button 4 The following empty form will appear From Relation La Ea a To Explanation 5 Using the lookup boxes locate the fragments you wish to join as well as a relation value if you wish to enter that as well 6 Enter an explanation for the relation 7
44. se 1 To create a new knowledge base select Admin gt Create KB The following dialog pox pops up Build new Knowledge Base Knowledge Base Details Knowledge hase name Knowledge base namespace KB build script org neuroscholar v1 tte T NySQL Administration Root Login Root Password Permissions View Indexes View Data Edit Data User e a Everyone e 1 om cancel The system automatically fills in the details of the Knowledge base namespace which is the name of the computer being used The user is required to fill in the Knowledge Base name and select the type of KB they desire within this release only the www neuroscholar v1 core is available 2 Fill in the root login and password The user may also set the permissions for this knowledge base restricting who may or may not access or edit the data in the system 3 Hit Ok A small progress monitor dialog will pop up and when this is complete you should be in the Home state for an empty KB with the correct name and design 6 2 Destroying a knowledge base 1 Select Admin gt Destroy KB The following dialog pox pops up amp Remove Knowledge B 2 Select one of the listed systems then hit the Destroy button 3 Confirm your root status by logging in as root 4 Then the system will drop the relevant database from within the underlying MySQL system Note that this permanently deletes all data in that
45. tions from the ventromedial nucleus of the hypothalamus a Phaseolus vulgaris leucoagglutinin study in the rat J Comp Neurol 348 41 79 Canteras Simeri Swanson 1995 Organization of projections from the medial nucleus of the amygdala a PHAL study in the rat J Comp Neurol 560 213 45 Canteras Swanson 1992 Projections of the ventral subiculum to the amygdala septum and hypothalamus a PHAL anterograde tract tracing study in the rat J Comp Neurol 924 180 94 Goto Swanson Canteras 2001 Connections of the nucleus incertus J Comp Neuro 430 06 122 Thompson Canteras Swanson 1996 Organization of projections from the dorsomedial nucleus of the hypothalamus a PHA L study in the rat J Comp Neurol 376 143 73 Total 7 records urrent KB Gullyjen Logged as root admin 5 1 5 Display The view when displayed appears in a form with the same structure as the query form with the fields filled in At the top left are links to the views parents which when clicked provide show the same view in the form of the parent The index string of the view appears at the top of the form Knowledge Base Guliy jcn w DISPLAY Article J come Neurol 24 743 79 Initials Surname NS canteras Connections ofthe posterior nucleus ofthe amygdala Journal E Comp Neurol Y Volume Issue Pages 143 79 ere also identified The efferent projections ofthe PA as determined with the PHAL method ap
46. users should use shift click where right click is mentioned in the text 1 e hold the shift key down whilst clicking with the mouse The screen shot shown above illustrates the main concepts required to understand the components of the graph shown in the View Definition panel e Each node is a separate view Data views have oval borders with an accompanying icon whereas relation views have no borders e Children are connected to their parents by green inheritence arrows e Simple constitutive links between views that are blue tapering arrows not shown in screenshot e Dependent views are connected to the views they depend on by red dashed arrows e Relations have one input and one output but they have the same view for both Double clicking on a node brings it to the center and opens all links to it Right clicking a node brings a number of options depending on the type of node and whether the user is logged in If the user has not logged in all options available here are simply display functions The user may view documentation which takes them to the Documentation state this view The user may also run a query for the specific type of view Note that the Expand Collapse Hide Center Node functions all have a superficial effect on the view graph by permitting the user to remove specific items from view temporarily This is not the same as the system s visibility controls which will be described presentl
47. voice recordings or structured attribute value pairs Users may also use download references and PDF files rapidly from within the application to make interacting with the literature as straightforward as possible 3 The NeuroScholar License NeuroScholar is open source software meaning that we make the source code available for perusal modification and redistribution where required We have adapted the GNU General Public License stating that any work derived from NeuroScholar must also be distributed as an open source project This is quite restrictive but is suitable for academic work ensuring that our software solution supports open sharing and distribution of source code 4 System set up For the first time the system is now available as an installation package Users need only download the package double click it and then follow instructions to have NeuroScholar operational on their system Note that you must also install MySQL and you must know the root login and password 4 1 Release 0 001 some additional installation and setup required Due to a minor bug it is currently necessary to download and install GhostScript to ensure full system functionality Ghostscript may be downloaded from http www cs wisc edu ghost doc AFPL On running the system for the first time users should configure the system selecting File gt Configure A dialog box will pop up with the following structure Tool Configuration
48. xcerpt and select Delete Excerpt to delete the excerpt 8 Click the Plugin toggle button this shows the data associated with this fragment When no annotations are entered the statement that is entered into the system is the enclosed text delineated within the paper itself amp NeuroScholar Knowledge Browser aaa Application Admin cranh Help E Login root Password eevee F MA Knowledge Base Gullyiwattstab INSERT Acher Teler Azerad Brabel Fago Pin 7997 fowl AGR P EFhe four stereolsomer nowledgestatement f aminocyciopentane 1 3 4 friearboxylic acid 18 ana ii 19 3RARIAN 3 20 an Fragment S5 45 A 200 have been synthesized and evaluated for their effects af glutamat BibliographicFragment recepfors subfyoes ACP Ts are ACPO analogues in Which a Cid carboxylic grouo As added af posifion in fhe cyclopentane ring p1 ACPT The four stereoisomers of Statement 1M aminocyclopentane 1 3 4 tricarboxwlic acid 18 and lIl 019 SR 4F 111 E 4 20 and 35 451 5 20 have been synthesized and evaluated for their Citation lte between metabotropic glutamate receptor subtypes et Med Chem 40 31 1 9 29 Dat 1 y Wariable Value Units Page Annotation Excerpts 1 Pp urrent KE Gullyiwattslab Logged in as root admin 6 Click the commitinsert button to upload the fragment into the knowledge base 8 7 Insert a fragment with annotations either text voice 1 F
49. y Note that if nodes have been loaded into the application s memory but are temporarily hidden a small red box will appear on the top right edge of the node with the number of neighboring hidden nodes If the user has logged in the user may also insert an instance of the view Note that this option does not appear if the view being clicked has dependencies e g the BibliographicFragment view definitions and its children are dependent on the Article view If the user selects Importance from the popup menu a small box with five stars appears displaying the relative importance of this view definition when prioritizing views for reliability note that this feature is still under development Note that in this case relation nodes have identical behavior except that they do not permit users to enter or view Importance data It is possible to temporarily remove an edge from the graph by right clicking it and selecting Hide Edge from the popup menu If a user right clicks the background of the viewgraph definition panel a Toggle Controls popup menu will appear If this is selected the controls shown in the figure appear These controls are generic to the TouchGraph interface and can be manipulated to control the appearance of the overall graph The Zoom control scales distances within the graph so that nodes lies closer together or further apart The Rotate control spins the whole graph T
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