URL Search documentation

The CoCoMac online interface provides a utility to create web URL links that automatically search and retrieve information from CoCoMac. These URL links can be constructed manually according to the specification below.

You may generate a query and submit it to CoCoMac providing that proper attribution is given to the Computational | Systems | Neuroscience group and CoCoMac, e.g. citing the following paper:

Kötter R. (2004) Online retrieval, processing, and visualization of primate connectivity data from the CoCoMac database, Neuroinformatics, 2: 127-144.

If you place such a query on your web site it must be clear to users that the search is actually being conducted at the CoCoMac database server. When you link to CoCoMac, present CoCoMac in a separate browser window so that users can easily return to your page as well as go directly to CoCoMac.

General instructions

A URL querying CoCoMac consists of the CoCoMac address, User, Password, Search category, further optional Parameters, and a Search string as in the following general specification:

http://CoCoMac-address/URLSearch.asp?user=User&password=Password &Search=SearchCategory&Parameters &SearchString=Search string

Space (‘ ‘)inside the search string can sometimes produce problems and should be eliminated or filled in by a plus (‘+’).

CoCoMac address

Begin the URL with the CoCoMac address.

cocomac.org/

Note that the current server at http://cocomac.org is much faster than the one previously used during the development stage (http://www.mon-kunden.de/cocomac/). Therefore the use of the previous server is not advised. Also, the data available from different servers may not be equally up-to-date.

The starting page for the manual online interface remains to be at http://www.cocomac.org. This provides us some flexibility with technical changes and with the presentation of additional information.

To initiate the URL search this address is followed by

URLSearch.asp?

Search category

Then follows the search category

Search=Search category

where Search category is one of

Literature

Connectivity (or Connections)

Mapping (or Relations)

Search category is required.

Username and userpassword

User=user

Password=password

User and Password are required. You can create a username and userpassword at www.cocomac.org. There is no charge for registering or using cocomac. The use of the example user=cocomac and password=cocomac is discouraged since multiple simultaneous requests by the same user may lead to retrieval errors.

Search Parameters

Most parameters are optional, i.e. if these are not supplied then CoCoMac uses internal default values.

Some parameters apply to all Search categories

OutputType=OutputType

Dispmax=Number

ItemsPerPage=Number

SortOrder=SortOrder

SortBy=SortCriterion

Tool=Toolname

OutputType is one of

XML_Browser

XML_Email

HTML_Browser

HTML_Printer

Note that the OutputType to be chosen for automated processing of XML via http queries is XML_Browser even if the XML output is not to be shown in a browser window.

Number is a positive integer defining the maximum number of returned items or the maximum number of items per page as in

Dispmax=All

ItemsPerPage=20

Currently, the highest number of items displayed for Dispmax or ItemsPerPage is 32767.

SortOrder is either ascending (asc) or descending (desc)

SortOrder=asc

SortCriterion depends on the chosen Search category

SortBy=SourceMap

Tool is a requested option for automatically generated URL searches. This identifies to our online interface the software tool used for generating the URL strings and allows us to offer customised services. Example:

Tool=Caret

Connectivity

Specific Parameters for the Search category Connectivity are

DataType=DataType

where DataType is one of

PrimaryProjections or PrimProj

IntegratedPrimaryProjections or IntPrimProj

Data of two further DataTypes in the category Connectivity are under development and are currently not available for general use (for definitions of these data types see Stephan et al. 2001 Phil. Trans. R. Soc. Lond. B).

ResultingProjections or ResProj

IntegratedResultingProjections or IntResProj

Mapping

Specific Parameters for the Search category Mapping are

DataType=DataType

where DataType is one of

PrimaryRelations or PrimRel

IntegratedRelations or IntRel

A further DataType in the mapping category is under development and is currently not available for general use (for definitions of these data types see Stephan et al. 2001 Phil. Trans. R. Soc. Lond. B).

ResultingRelations or ResRel

Search string

The Search string consists of one or more Criteria to be matched against the database contents. These Criteria are concatenated by the Boolean operators

AND

NOT

The Criteria are specific to the Search category. They are preceded by the Search Term in the format

(‘Search Term’)[Criterion]

All criteria that are available via the manual user interface at http://www.cocomac.org can be used in automated searches via URL strings. The same criterion can be used repeatedly in the search string and priorities in the Boolean concatenation can be expressed by brackets ().

Connectivity

For Connectivity the Search String may contain the following Criteria

Keywords

SourceMap

TargetMap

SourceSite

TargetSite

Density

SourceHemisphere

TargetHemisphere

FibreCourse

PDC_SourceSite

PDC_TargetSite

PDC_Density

as, for example, in

('prefrontal') [Keywords]

('FV91') [SourceMap]

('DU86') [TargetMap]

('FST') [SourceSite]

('PP' EXT 'I,L') [TargetSite]

('3') [Density]

('Left') [SourceHemisphere]

('Left' OR 'Right' OR 'Unknown') [TargetHemisphere]

('Ipsilateral') [FibreCourse]

('A') [PDC_SourceSite]

('A' OR 'C' OR 'D' OR 'F' OR 'H' OR 'L') [PDC_TargetSite]

('A' OR 'C' OR 'D' OR 'F' OR 'H' OR 'J') [PDC_Density]

Mapping

For Mapping the Search String may contain the following Criteria

Keywords

SourceMap

SourceSite

TargetMap

TargetSite

RelationCode

PDC_Relation

as, for example, in

('thalamic') [Keywords]

('O52') [SourceMap]

('J85') [TargetMap]

('MDdc') [SourceSite]

('CL' EXT 'I,L') [TargetSite]

('I' OR 'S' OR 'L' OR 'O') [RelationCode]

('A' OR 'C' OR 'D' OR 'F' OR 'H' OR 'J' OR 'L' OR 'N') [PDC_Relation]

(Note that RelationCode is replaced by PathCategory for the DataType ResultingRelations)

Literature

For Literature the Search String may contain the following Criteria

Keywords

Author

Year

Title

JournalRef

Journal

LitID

PMID

LiteratureType

DataType

BrainMap

BrainSite

BrainSiteClass

TracerSubstance

as, for example, in

('premotor') [Keywords]

('Barbas, H') [Author]

('>1990') [Year]

('Subcortical projections of area MT in the macaque') [Title]

('J. Comp. Neurol., v169, p371-392 ') [JournalRef]

('J. Comp. Neurol.') [Journal]

('PHT00') [LitID]

('410102') [PMID]

('J' OR 'C') [LiteratureType]

('mapping') [DataType]

('FV91') [BrainMap]

('V1') [BrainSite]

('Area_IsoCtx ') [BrainSiteClass]

('WGA-HRP') [TracerSubstance]

Examples of URL search strings

The following URL retrieves an XML formatted list of all areas in the partitioning scheme of Felleman & Van Essen 1991:

http://cocomac.org/URLSearch.asp?user=cocomac&password=cocomac&Search=Literature&OutputType=XML_Browser&SearchString=('FV91') [BrainMap]

The following URL retrieves a list of all areas in the partitioning scheme of Brodmann 1909 and displays it in a browser window:

http://cocomac.org/URLSearch.asp?user=cocomac&password=cocomac&Search=Literature&OutputType=HTML_Browser&SearchString=('B09')[BrainMap]

The following retrieves a list of mapping information for area 8B of Walker 1940, showing that some authors regard this area as a subarea of area 9:

http://cocomac.org/URLSearch.asp?user=cocomac&password=cocomac&Search=Mapping&DataSet=PRIMREL&OutputType=HTML_Browser&SearchString=('W40')[SourceMap]AND('8B')[SourceSite]

Is there a connection from area 3b (somatosensory cortex) to area 4 (primary motor cortex)? The answer is that such a connection has been shown but not all tracer injections delivered a positive result:

http://cocomac.org/URLSearch.asp?user=cocomac&password=cocomac&Search=Connectivity&DataSet=PrimProj&OutputType=HTML_Browser&SearchString=('3b')[SourceSite]AND('4')[TargetSite]

Here is a more elaborate example: The following URL retrieves all none-0-density afferents and efferents of Brodmann’s area 2 in original literature reports and displays them in a browser:

http://cocomac.org/URLSearch.asp?user=cocomac&password=cocomac &tool=BrainInfo&Search=Connectivity&DataSet=PrimProj&OutputType=HTML_Browser&SearchString=(('B09')[SourceMap]AND ('2%231')[SourceSite] OR ('B09')[TargetMap]AND ('2%231')[TargetSite]) AND NOT ('0')[Density]

If you think that the few results returned cannot be everything then consider that modern tracing studies rarely use Brodmann’s map. You might want to relax the criterion to find connections of any cortical area 2:

http://cocomac.org/URLSearch.asp?user=cocomac&password=cocomac &tool=BrainInfo&Search=Connectivity&DataSet=PrimProj&OutputType=HTML_Browser&ItemsPerPage=40&SearchString=(('2%231')[SourceSite] OR ('2%231')[TargetSite]) AND NOT ('0')[Density]

The following URL retrieves an XML formatted list of all connections between areas in the partitioning scheme of Felleman & Van Essen 1991 as listed in the PrimaryProjections (this query make take a few minutes to produce results. If it does not work at http://cocomac.org then try http://mon-kunden.de/cocomac):

http://cocomac.org/URLSearch.asp?user=cocomac&password=cocomac&Search=Connectivity&DataSet=PrimProj&OutputType=XML_Browser&SearchString=('FV91')[SourceMap]AND('FV91')[TargetMap]

Here is a more complex example retrieving connections between areas defined in two different papers by Matelli and colleagues (this currently does not work at http://cocomac.org but at http://mon-kunden.de/cocomac):

http://cocomac.org/URLSearch.asp?user=cocomac&password=cocomac&Search=Connectivity&DataSet=IntPrimProj&OutputType=XML_Browser&SearchString=(('MLR91')[SourceMap]OR('MLR85')[SourceMap])AND(('MLR91')[TargetMap]OR('MLR85')[TargetMap])

The following URL retrieves an XML formatted list of all efferents from any brain site named 23 as listed in the IntegratedPrimaryProjections and displays them in the browser in XML format (this currently does not work at http://cocomac.org but at http://mon-kunden.de/cocomac):

http://cocomac.org/URLSearch.asp?user=cocomac&password=cocomac&Search=Connectivity&DataSet=IntPrimProj&OutputType=XML_Browser&SearchString=('23') [SourceSite]

The following URL retrieves an XML formatted list of all efferents from any brain site named 10 as listed in the Resulting Projections and displays them with the TransformationPath for the SourceSite in a browser in XML format. CAVE: In the details you have to specify the parameter ‘TP_sourcesite’ and also the parameters ‘IntPrimProj’ and ‘ResProj’ to retrieve the Transformation Path information; or use details=ALL. The output in this example was limited to 5 items. (This query requires developer status and does not work for the user cocomac!):

http://cocomac.org/URLsearch.asp?user=cocomac&password=cocomac&Search=Connectivity&DispMax=5&DataSet=ResProj&OutputType=XML_Browser&SearchString=('10')[SourceSite]&Details=ResProj,IntPrimProj,TP_sourcesite

http://cocomac.org/URLsearch.asp?user=cocomac&password=cocomac&Search=Connectivity&DispMax=5&DataSet=ResProj&OutputType=XML_Browser&SearchString=('10')[SourceSite]&Details= ALL

Further comments

The search syntax is not case sensitive (except for Boolean operators)
The search syntax is not order sensitive
Space (‘ ‘) between the elements of a URL search should be eliminated or filled in by a plus (‘+’) or ‘%20’.
The hash sign (‘#’) designates a target in html and must therefore be replaced by ‘%23’

URL search systematics

(Should be defined in XML schema!!!)

Search category	Parameter	Default value	Other values
Connectivity
	DataSet	PrimProj	IntPrimProj ResProj IntResProj
	Details	None	ResProj IntPrimProj PrimProj LitRef (XML only) Comments TP_sourcesite, TP_targetsite (this requires DataSets IntResProj and ResProj) All
	Sortby	SourceMap	SourceSiteAcronym TargetSiteAcronym TargetMap Density PDC_SourceSite PDC_TargetSite PDC_Density Hemisphere_SourceSite Hemisphere_TargetSite Course

	User	- (required)
	Password	- (required)
	ItemsPerPage	20	All
	DispMax	32767	All
	Sortorder	asc or ascending	desc or descending
	OutputType	XML_Browser	HTML_Browser HTML_Printer XML_Email
	Tool	-	e.g. BrainInfo or Caret
Mapping
	DataSet	PrimRel	IntPrimRel ResRel
	Details	None	IntPrimRel (only for ResRel) PrimRel (only for IntPrimRel and ResRel) Comments All
	Sortby	0	SourceSiteAcronym SourceMap TargetSiteAcronym TargetMap RelationCode PDC_Relation LitID (only for PrimRel and XML)
Literature
	Details	Status, BrainSites, Methods, Injections	Relations LabelledSites Comments None All
	Sortby	Year	Author Reference LiteratureType (LitID)

Search String composition

SearchCategory	Criterion	Valid values
Connectivity	Keywords	String
	SourceSite	String
	SourceMap	String
	TargetSite	String
	TargetMap	String
	Density	0, 1, 2, 3, X
	SourceHemisphere	R, L, U
	TargetHemisphere	R, L, U
	FiberCourse	I, C, U
	PDC_SourceSite	Letter
	PDC_TargetSite	Letter
	PDC_Density	Letter
Mapping	Keywords	String
	SourceSite	String
	SourceMap	String
	TargetSite	String
	TargetMap	String
	RelationCode	I, S, L, O, E, C
	PathCategory	1..5, 11..15, 21..25
	PDC_Relation	Letter
Literature	Keywords	String
	Author	String
	Year	Year or Range (e.g. '>1905' AND '<1919')
	Title	String
	JournalRef	Journal, Volume, pages (e.g. 'Hippocampus, v5, p511-533')
	Journal	String
	LitID	String
	PMID	Number
	LiteratureType	J (=Journal), B (=Book), C (=book Chapter)
	DataType	Mapping, Connectivity
	BrainMap	String
	BrainSite	String
	BrainSiteClass	Area_IsoCtx, Area_AlloCtx, Lamina_Ctx, Lamina_SubCtx, Nucleus_SubCtx
	TracerSubstance	String