The Resource Description Framework (RDF) is an imported schema that allows the encapsulation of metadata.

The entity element

The entity element encapuslates one instance of a domain or in the case of mapping a PDB chain or UniProt sequence.

Format:

The segment defines a continuous region of an entity. Two or more segments can be used to model discontinuous domains. In the mapping section where chains in PDB where they map to more than one UniProt sequence (e.g. Chimeras). Note, this does not reflect disordered PDB regions as they are continous but not observed. Problems may arise from PDB numbering system...... as a start Resnum of -1 to a end Resnum of 10 does not mean that there are 12 residues involved!! Thus, we strongly recommend that you cross map structural domains to MSD numbering.

Format:

A container for a set of residue elements

Format:

The residue element allows description/information and cross mappings to other databases about a single residue to be conveyed.

Format:

<residue 
	dbResNum="The residue number" 
	dbResMon="The residue name" >
		<crossRefDb 
			dbSource="the database being cross referenced" 
			dbVersion="The cross referenced database version" 
			dbCoordSys="The cross referenced database co-ordinate system" 
			dbAccessionId="The cross reference database identifier" 
			dbResNum="cross referenced residue number" 
			dbResName="cross referenced residue name" 
			dbChainId="cross referenced chain id/"> 
		<residueDetail 
			dbSource="the infromation source" 
			property="the property that the CDATA refers to">
				information about the residue 
		</residueDetail>
</residue>	

Element:<residue>

The residue element describes information about the residue.

attributeGroup:resRef

attribute:dbResNum

(required). The database residue number.

attribute:dbChainId

(optional). This is used to specify a chain id when using a PDB based co-ordinate system. e.g. dbChainId="A"

attribute:dbResName

(required). The name of the residue. In the UniProt system methionine is M, whereas in PDBresnum system it is MET.

Element:<crossRefDb>

Allows the defined residue to be cross referenced to another database.

attributeGroup:dbRef

This attribute group is used for referring to a database.

attribute:dbSource

(required). The name of the database.

attribute:dbVersion

(required). The version of the database or of the entry (e.g. PDB REVDAT). The date sgould be in the format YYYY-MM-DD.

attribute:dbCoordSys

(optional). The co-ordinate system used by the database. This is not always the same as the database. For example, Pfam uses UniProt as an underlying co-ordinate system.

attribute:dbAccessionId

(required). The database entry accession id. For example, SCOP have sunid, Pfam accessions(PF01020).

attributeGroup:resRef

attribute:dbResNum

(required). The database residue number.

attribute:dbChainId

(optional). This is used to specify a chain id when using a PDB based co-ordinate system. e.g. dbChainId="A"

attribute:dbResName

(required). The name of the residue. In the UniProt system methionine is M, whereas in PDBresnum system it is MET.

Element:<residueDetail>

Describes some information about the residue. For example Not_observed or active_site.

attributeGroup:detail

The following attributes are bundled together to form a group of attributes that are capable of describing additional information about a particular node.

attribute:dbSource

(required). The database where the information about this source orginates.

attribute:property

Allows a part of the segment to be mapped to another database.

Format:

<listMapRegion>
	<mapRegion 
		start="The start point being mapped" 
		end="The end point being mapped";>
			<db dbSource="the database being mapped referenced" 
				dbVersion="The mapped database version" 
				dbCoordSys="The mapped database co-ordinate system" 
				dbAccessionId="The mapped database identifier" >	

				dbChainId="The co-ordinate system chain id" 
				start="The start point being mapped" 
				end="The end point being mapped";>
				<dbDetail 
					dbSource="the infromation source" 
					property="the property that the CDATA refers to">
							information about the mapping or mapped database 
				</dbDetail>
			</db>
		</mapRegion>
</listMapRegion>

Element:<listMapRegion>

(optional, once only when used). The element contains a list of regions from within the segment that map to other databases.

Element:<mapRegion>

(required, one or more). Defines a region from within the segment that one wished to map to.

attributeGroup:region

The following attributes are bundled together to form a group of attributes that are capable of defining a region on something using a predefined co-ordinate system.

attribute:start

(optional). The start co-ordinate.

attribute:end

(optional).The end co-ordinate.

Element:<db>

(required, once only). Provides the cross reference to the defined mapRegion.

attributeGroup:dbRef

This attribute group is used for referring to a database.

attribute:dbSource

(required). The name of the database.

attribute:dbVersion

(required). The version of the database or of the entry (e.g. PDB REVDAT). The date sgould be in the format YYYY-MM-DD.

attribute:dbCoordSys

(optional). The co-ordinate system used by the database. This is not always the same as the database. For example, Pfam uses UniProt as an underlying co-ordinate system.

attribute:dbAccessionId

(required). The database entry accession id. For example, SCOP have sunid, Pfam accessions(PF01020).

attribute:<dbChainId>

(optional). This is used to specify a chain id when using a PDB based co-ordinate system. e.g. dbChainId="A". In the case of unlabelled chains, the standard representation expected is " ".

attributeGroup:region

The following attributes are bundled together to form a group of attributes that are capable of defining a region on something using a predefined co-ordinate system.

attribute:start

(optional). The start co-ordinate.

attribute:end

(optional).The end co-ordinate.

Element:<dbDetail>

(optional, one or more). Describes some information about the database or the mapped region in that databse. For example an alternative name.

attributeGroup:detail

The following attributes are bundled together to form a group of attributes that are capable of describing additional information about a particular node.

attribute:dbSource

(required). The database where the information about this source orginates.

attribute:property

This part of the schema allows the modeling of alignments, whether they are structural or sequence based. The objects that are aligned should be defined in the entity section of the alignment. However, there is no cross validation built into the schema. Admittedly, there is some redundancy in this part of the schema as the alignment schema is imported into both the eFamily schema and the dasalignment schema. Although slightly different methods underly the way alignments are accessed, there is little point in reinventing the wheel to produce an alignment section. Also, once the code is written to export the alignments, it can be used to produce dasalignments or eFamily alignments.

Format:

	<alignment>
	<alignObject dbAccessionId="someid" 
		objectVersion="version" intObjectId="internalId" type="
		objectType" dbSource="someSouce" 
		dbVersion="version" dbCoordSys="coords"  >
		<alignObjectDetail dbSource="someSouce" 
		property="property">
			some details about the object. e.g. description, etc. 
		</alignObjectDetail> 
		<sequence>
			SEQUENCESEQUENCESEQUENCE
		</sequence>	
	</alignObject>
	<score methoName="scorename" value="scorevalue">
	<block blockScore="score" blockOrder="position"> 	
		<segment intObjectId="intObjectId" start="start" end="end" orientation="+">
			<cigar>9I5M10D</cigar>
		</segment>
	</block> 	
	<geo3D intObjectId="intObjectId">
		<vector x="xCoord" y="yCoord" z="zCoord"/>
		<matrix>
			<max11 coord="float"/>
			<max12 coord="float"/>
			<max13 coord="float"/>
			<max21 coord="float"/>
			<max22 coord="float"/>
			<max23 coord="float"/>
			<max31 coord="float"/>
			<max32 coord="float"/>
			<max33 coord="float"/>
		</matrix>
	</geo3D>	
	</alignment>

	

Element:<alignment>

(optional; one or more when used) everything below belongs to an alignment.

Element:><alignObject>

(required; two or more) A description of the objects that are aligned.

attribute:objectVersion

(required) version of Object. e.g. CRC64 checksum for protein sequences.

attribute:intObjectID

(required) internal, unique name name for this object. This is used in the SEGMENT section to identify to which object an alignment belongs to.

attribute:type

(optional) a type for this object.e.g. DNA, PROTEIN, STRUCTURE, etc.

attributeGroup:dbRef

This attribute group is used for referring to a database.

attribute:dbSource

(required). The name of the database.

attribute:dbVersion

(required). The version of the database.

attribute:dbCoordSys

(optional). The co-ordinate system of used by the database. This is not always the same as the database. For example, Pfam uses UniProt as an underlying co-ordinate system.

attribute:dbAccessionId

(required). The database entry accession id. For example, SCOP have sunid, Pfam accessions(PF01020).

Element:<sequence>

(optional; one) the sequence of this object. Clients generally should use the DAS - SEQUENCE request to get the seqeuence, so this is optional.

Element:<alignObjectDetail>

(optional; zero or more) details about the object

attributeGroup:detail

The following attributes are bundled together to form a group of attributes that are capable of describing additional information about a particular node.

attribute:dbSource

(required). The database where the information about this source orginates.

attribute:property

(required). A description of the CDATA. For example, if you wanted to give an alternative id for a database, e.g. a UniProt ID , then the <someDetail dbSource="UniProt" property="id">VAV_HUMAN</someDetail>

Element:score>

(optional; zero or more) a score for this alignment. an alignment can be described with several scores. each of the scores is described with the following

attributes:

attribute:methodName

(required) the name of the score, e.g. number of equivlanet residues (eqr), e-value, etc.

attribute:value (required) the value of the score e.g. 99, 10e-22 , etc.

Element:<block>

(required; one or more) a block of the alignment. an alignment can consist of one or more blocks. Often it will be only one block, since the CIGAR type of writing the alignment information allows to encode blocks.

attributes:

attribute:blockScore

(optional) some kind of score for a block

attribute:blockOrder

(required) The number of block in the alignment.

Element:<segment>

attributeGroup:region

The following attributes are bundled together to form a group of attributes that are capable of defining a region on something using a predefined co-ordinate system.

attribute:start

(optional). The start co-ordinate.

attribute:end

(optional).The end co-ordinate.

attribute:intObjectID

(required). The internal ID of the object.

attribute:strand

(optional). Strand of the object

Element:<cigar>

(optional). encoding of the alignment. The "cigar" string provides an efficient way to encode an alignment. 15M2D3I e.g. means that the 15 residues of the sequence are Matched (aligned), then there are 2 Deletions, followed by 3 Insertions. Since in some situations the alignment will just consist of an aligned block, the cigar string is optional. If it is missing the alignment is ungapped and ranges from "start" to "end" of the SEGMENT.

Element:<geo3D>

(optional) geometrical operation on 3D object. if the objects to be aligned are three dimensional objects this section defines how one of the needs to be shifted and rotated in order to be superimposed with the others.

attribute:intObjectID

(required) The internal ID of the object.

Element:<vector>

(required, one) the shift vector the x,y, and z attributes are describing the shift vector.

Element:<matrix>

the "container" for the rotation matrix elements. ><max11> - <max33> the rotation matrix

Summary

Some Examples