Take a look at Tinkerpop's blueprints for a well tested Java API and 
Archimedes for simple graph operations in Clojure. 
http://www.tinkerpop.com/
https://github.com/clojurewerkz/archimedes

As far as the suggested protocols go, I would suggest doing something 
useful with them before opening it up to the community for comments. 
There's not much there to discuss in terms of merits or anything else. 
-Zack

On Monday, June 17, 2013 4:14:34 PM UTC-4, dgrnbrg wrote:
>
> I think that there's already a project working on this called Loom. The 
> furthest-developed fork is here: https://github.com/aysylu/loom which 
> appears to have protocols for graphs, bindings to Titanium (the 
> Clojurewerkz graph DB library), visualization support, and implementations 
> of several algorithms.
>
> Maybe there's a way to incorporate these projects?
>
> On Monday, June 17, 2013 3:38:45 PM UTC-4, Stephen Kockentiedt wrote:
>>
>> Hello,
>>
>> I want to create a graph API similar to what core.matrix is for matrices. 
>> I have created some protocols which every graph implementation has to 
>> satisfy and a prototype implementation. Now I want your feedback on these 
>> protocols. Which functions do you want to see which aren't there? Which 
>> functions should be changed? Are there problems with the general design? 
>> Have you any other feedback?
>>
>> Here are the protocol definitions:
>>
>> (defprotocol PGraph
>>   "Minimal functionality of a graph."
>>   (directed? [g]
>>     "Returns true if the graph is directed and false if the
>>      graph is undirected. If it is undirected, all functions
>>      taking two nodes must be commutative with regard to
>>      these nodes.")
>>   (nodes [g]
>>     "Returns a set or sequence of all nodes of the graph. May
>>      not contain duplicates.")
>>   (has-edge? [g n1 n2]
>>     "Returns true if the graph g has an edge from node n1
>>      to node n2.")
>>   (direct-successors [g n]
>>     "Returns a set or sequence of all nodes n2 for which
>>      (has-edge? g n n2) returns true. May not contain
>>      duplicates."))
>>
>> (defprotocol PPredecessorGraph
>>   "Optional functionality of a graph which can give a
>>    list of all direct predecessors of a node."
>>   (direct-predecessors [g n]
>>     "Returns a set or sequence of all nodes n2 for which
>>      (has-edge? g n2 n) returns true. May not contain
>>      duplicates."))
>>
>> (defprotocol PEditableGraph
>>   "Minimal functionality of an editable graph."
>>   (mutable? [g]
>>     "Returns true if the graph is mutated in place.
>>      If true is returned, the other functions change
>>      the graph passed as the first argument and return
>>      the same graph object. If false is returned, the
>>      functions return a new graph and the old graph is
>>      unchaged.")
>>   (add-node [g n]
>>     "Adds the node n to the graph g. If it already
>>      contained n, the graph will not be changed.")
>>   (remove-node [g n]
>>     "Removes the node n from the graph g. If it did
>>      not contain n, the graph will not be changed.")
>>   (add-edge [g n1 n2]
>>     "Adds an edge from node n1 to node n2 to the graph g.
>>      If one or both of the nodes is not present it will
>>      be added to the graph. If the edge was already present,
>>      the graph will not be changed.")
>>   (remove-edge [g n1 n2]
>>     "Removes the edge from node n1 to the node n2 from
>>      the graph g. If it did not contain the edge, the graph
>>      will not be changed."))
>>
>> (defprotocol PWeightedGraph
>>   "Functionality of a graph whose edges can be weighted."
>>   (edge-weight [g n1 n2]
>>     "Returns the weight of the edge from node n1 to
>>      node n2."))
>>
>> (defprotocol PEditableWeightedGraph
>>   "Functionality of a weighted graph whose weights can be
>>    changed."
>>   (update-edge-weight [g n1 n2 f]
>>     "Updates the weight of the edge from node n1 to node n2,
>>      where f is a function taking the old value and returning
>>      the new one. If the graph did not contain the edge, it
>>      will be created."))
>>
>> (defprotocol PNodeDataGraph
>>   "Functionality of a graph which stores data with its
>>    nodes."
>>   (node-data [g n]
>>     "Returns the data of the node n."))
>>
>> (defprotocol PEditableNodeDataGraph
>>   "Functionality of a graph which stores editable data
>>    with its nodes."
>>   (update-node-data [g n f]
>>     "Updates the data of the node n, where f is a function
>>      taking the old value and returning the new one. If the
>>      graph did not contain the node, it will be added."))
>>
>> (defprotocol PEdgeDataGraph
>>   "Functionality of a graph which stores data with its edges."
>>   (edge-data [g n1 n2]
>>     "Returns the data of the edge from node n1 to node n2."))
>>
>> (defprotocol PEditableEdgeDataGraph
>>   "Functionality of a graph which stores editable data
>>    with its edges."
>>   (update-edge-data [g n1 n2 f]
>>     "Changes the data of the edge from node n1 to n2, where
>>      f is a function taking the old value and returning the
>>      new one. If the graph did not contain the edge, it will
>>      be added."))
>>
>

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