MeV is capable of sending and receiving expression and annotation data within the Gaggle framework of bioinformatics applications. As of v4.5, MeV will broadcast certain pre-defined metadata tags in addition to the matrix, namelist and network data. It will also look for these tags when receiving broadcasts.
See the general information on using MeV in the Gaggle framework
Example metadata structure for a matrix broadcast:
metadata-root
|
|-> identifier-type: PROBE_ID
|-> MeV-metadata
|--> data-type: intensity
|--> array-name: affy_HG-U133A
|--> algorithm-source: HCL
|--> log-status: unlogged
Example metadata structure for a namelist broadcast
metadata-root
|
|-> identifier-type: ENTREZ_ID
|-> user-interactive: false
|-> MeV-metadata
|--> algorithm-source: KMC
For all broadcasts, MeV will include within the Metadata tuple a single called "MeV-metadata". All MeV-specific metadata will reside in this Tuple. Some metadata items will be included only in matrix broadcasts, while others will be included in namelists as well. Currently, no additional Metadata beyond a placeholder "MeV-metadata" item is included in Network broadcasts. When receiving a broadcast, MeV will attempt to locate and use these metadata items as well. The function of each item is described in its individual section, below.
Data type (matrix only, inbound and outbound broadcasts)
data-type: "ratio" | "intensity" This field indicates the type of data included in a matrix broadcast. An incoming broadcast including the "ratio" value will be interpreted as a two-color array, and loaded into the appropriate data structure. A broadcast with a data type of "intensity" will be treated as a single color, or intensity-based array, such as an Affymetrix array. The main noticeable difference between these two will be in the color scaling that MeV applies to its heatmaps. When MeV accepts an incoming matrix broadcast, it assumes that the data is of type "intensity" unless the data-type value indicates otherwise.
Array name (matrix only, outbound broadcast only)
array-name: affy_HG-U133A | affy_HG_U95E | TIGR_25K_Mouse_Set | etc. This field indicates the name of the array that MeV has stored for the broadcast dataset. This field will only be included if MeV's automatic annotation loader has been used to load the data. MeV currently does not act on this data if it is received as part of a broadcast. In the future, we hope to allow MeV to auto-load annotation for an incoming set of data using this array name. The names should match an array available on the Resourcerer ftp site.
Algorithm source (matrix and namelists, outbound broadcast only)
algorithm-source: KMC | HCL | etc. This value indicates the source (within MeV) of the dataset being broadcast. This will most often be an algorithm name, though it will sometimes not be populated.
User Interactive (Namelists only, inbound broadcast only)
user-interactive: true | false When receiving an incoming namelist broadcast, this flag determines whether MeV will ask the user to validate the incoming list of genes or will attempt to coerce the genes in the namelist into a cluster without user interaction. Cluster colors and names will be automatically assigned, and the identifier is required.
Identifier Type (matrix and namelists, inbound and outbound broadcasts) identifier-type: ENTREZ_ID | UNIGENE_ID | GENE_SYMBOL | REFSEQ_ACC | etc. For incoming broadcasts, this field indicates which of the supported MeV annotation types is used as an identifier in the incoming broadcast. This value will often be the same as the row titles title of the broadcast. This value will be used to inform MeV of the identifier type of incoming broadcasts and bypass certain user-interactions when receiving namelists.
Log-status (matrix only, inbound and outbound broadcasts)
log-status : unlogged | log2 | log10 This field indicates whether the data in the matrix has been log-transformed. The information is stored in MeV's data model. It is currently unused but in the future will be used by several of MeV's component modules.
