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Application programming interface
Introduction to the API
We offer an application programming interface (API) to allow data from MANGO to be easily retrieved programmatically.
This service involves forming URLs sent to the server as a GET request. Server responses are returned as either HTML, XML or as text files (see different query methods below).
Query format
Fields
All field names and values need to be formatted into a URL, therefore they cannot contain spaces or special characters.
Some have also been shortened for convenience.
All field names and values are lower-case alphanumeric.
A list of field names and the possible values are described below.
PubMedID
Field name:
pmid
Value: A valid PubMedID.
Gene
Field name:
Value: A valid mouse GeneID. The Entrez GeneID used in the current release of the MANGO database.
geneidValue: A valid mouse GeneID. The Entrez GeneID used in the current release of the MANGO database.
[Note: The GeneID is frozen at each MANGO release. If the GeneID for a gene changes between releases, it will not be updated in MANGO retrospectively.]
Process / Outcome
Field name:
Value: Any of
processValue: Any of
[proliferation | differentiation | migration | neuritogenesis | axonogenesis | dendritogenesis | maturation | survival | expression | numbers | function]
Cell stage / Marker
Field name:
Value: Any of
cellstageValue: Any of
[nc | pc | t0 | t1 | pg | t2a | lpg | t2b | t3 | nn | in | ein | lin | mn | brdu | dcx | cr | cb | astr | olig | gc ]
according to the scheme below;
| nc | Adult neurogenic cell |
| pc | Precursor |
| t0 | Vertical astrocyte (Type 0) |
| t1 | Stem cell (Type 1) |
| pg | Progenitor |
| t2a | Undetermined progenitor (Type 2a) |
| lpg | Late progenitor |
| t2b | Determined progenitor (Type 2b) |
| t3 | Neuroblast-like cell (Type 3) |
| nn | New neuron |
| in | Immature neuron |
| ein | Early immature neuron |
| lin | Late immature neuron |
| mn | Mature neuron |
| brdu | BrdU immunoreactive cell |
| dcx | Doublecortin immunoreactive cell |
| cr | Calretinin immunoreactive cell |
| cb | Calbindin immunoreactive cell |
| astr | Astrocyte |
| olig | Oligodendrocyte |
| gc | Granule cell neuron |
Effect
Field name:
Value: Any of
effectValue: Any of
[positive | neutral | negative]
Evidence
Field name:
Value: Any of
processValue: Any of
[exp | protmanip | genemanip]
according to the scheme below;
| exp | Gene or protein expression |
| protmanip | Protein manipulation |
| genemanip | Gene manipulation |
Species
Field name:
Value: Any of
speciesValue: Any of
[mouse | rat | guineapig | monkey]
Type
Field name:
Value: Any of
typeValue: Any of
[invivo | exvivo | invitro]
Expression filter
Field name:
Value:
This option controls whether results are returned for the outcome field
This is a special case to avoid swamping results with high-throughput microarray and RNA-Seq data which may not be relevant for the search.
expressionValue:
[true | false]This option controls whether results are returned for the outcome field
expression.This is a special case to avoid swamping results with high-throughput microarray and RNA-Seq data which may not be relevant for the search.
Negative results filter
Field name:
Value:
This option controls whether ‘negative’ results are returned. Negative results are defined as absent (
negativesValue:
[true | false]This option controls whether ‘negative’ results are returned. Negative results are defined as absent (
effect = negative) for the process/outcome expression
or no change (effect = neutral) for all other processes.
Query construction
Queries are formed into a URL starting
http://mango.adult-neurogenesis.de/download/annotations?
followed by field name/value pairs joined by the symbol =
and separated by the symbol &.
Multiple values can be selected for each field by supplying a comma-separated list.
[Note: Multiple values are ONLY allowed for XML and text file downloads - NOT for HTML-formatted result tables.]
Return types
HTTP results tables
These requests return a web page showing an ‘annotations’ table as seen when browsing the website normally.
The results shown can be tuned using the search parameters as described above.
XML results tables
These requests return results from an ‘annotations’ database search as an XML document.
The structure of the XML document is as follows;
<mango:resultset xmlns:mango="http://mango.adult-neurogenesis.de/documents/api">
<mango:query-information>
<mango:database-version></mango:database-version>
<mango:result-count></mango:result-count>
<mango:expression-data-included></mango:expression-data-included>
<mango:negative-data-included></mango:negative-data-included>
</mango:query-information>
<mango:query-result>
<mango:annotation>
<mango:pmid></mango:pmid>
<mango:geneid></mango:geneid>
<mango:species></mango:species>
<mango:process></mango:process>
<mango:cellstage></mango:cellstage>
<mango:effect></mango:effect>
<mango:evidence></mango:evidence>
<mango:type></mango:type>
<mango:status></mango:status>
<mango:publicationfirstauthor></mango:publicationfirstauthor>
<mango:publicationyear></mango:publicationyear>
</mango:annotation>
</mango:query-result>
</mango:resultset>
Example: http://mango.adult-neurogenesis.de/xml/annotations?geneid=11423&cellstage=pc,in&effect=negative
Text files
These requests return results from an ‘annotations’ database search as a tab-delimited text file.
Example: http://mango.adult-neurogenesis.de/download/annotations?geneid=11423&cellstage=pc,in&effect=negative