Move text from Wiki to README

README

@@ -5,7 +5,7 @@ bioperl-network README
 3. Overview
 4. Status
 5. History
-
+6. Usage Notes
 
 1. Installation
 
@@ -15,11 +15,8 @@ bioperl-network.
 
 2. PSI Formats
 
-Different databases offer different variants of the PSI 2.5
-format. Some of these files cannot be parsed by this package. Please see:
-
-http://www.bioperl.org/wiki/Module:Bio::Graph::IO::psi_xml
-
+Different databases offer different variants of the PSI 2.5 format.
+Some of these files cannot be parsed by this package. Please see Usage Notes.
 
 3. Overview
 
@@ -65,9 +62,7 @@ work. Although the code is tested and stable it lacks functionality. Not
 all fields in the PSI MI standard are parsed into a network, for example.
 The BioPAX format is not parsed, arguably as important a format as
 PSI MI. In addition useful functions such as searching by sequence or 
-ontology term aren't yet implemented. If you are interested in contributing
-please contact Brian Osborne at bioperl-l@bioperl.org.
-
+ontology term aren't yet implemented.
 
 5. History
 
@@ -90,3 +85,28 @@ The advantages to using Graph are that Bioperl developers are not
 responsible for maintaining the code that actually handles graph
 manipulation and there is more functionality in Graph than in SimpleGraph.
 You must install version .86 of Graph, or greater.
+
+6. Usage Notes
+
+## HPRD
+
+Individual PSI XML files from HPRD can't be parsed as is because the fullName of the organism of an interacting protein is not specific. HPRD uses values like 'Mammalia' rather than the required species names, thus Bio::Species objects can't be constructed. Although I haven't performed an accurate count a simple grep suggests that there are thousands of interacting proteins labelled 'Mammalia'. Since HPRD says that it is concerned exclusively the human proteome it may that one can globally replace 'Mammalia' with 'Homo sapiens'. On the other hand it may be that including an interaction in HPRD is allowed when only one of the interacting pair is human, the definitive test could be performed using the identifiers (BIO 18:16, 31 December 2005 (EST)).
+
+Another thing to notice about HPRD's individual "PSI-MI" files is that they begin with various blocks like protein and interaction and the PSI entrySet section starts somewhere in the middle of the file. BIO 13:33, 23 January 2006 (EST).
+
+References
+
+Mishra GR, Suresh M, Kumaran K, Kannabiran N, Suresh S, Bala P, Shivakumar K, Anuradha N, Reddy R, Raghavan TM, Menon S, Hanumanthu G, Gupta M, Upendran S, Gupta S, Mahesh M, Jacob B, Mathew P, Chatterjee P, Arun KS, Sharma S, Chandrika KN, Deshpande N, Palvankar K, Raghavnath R, Krishnakanth R, Karathia H, Rekha B, Nayak R, Vishnupriya G, Kumar HG, Nagini M, Kumar GS, Jose R, Deepthi P, Mohan SS, Gandhi TK, Harsha HC, Deshpande KS, Sarker M, Prasad TS, and Pandey A. Human protein reference database--2006 update. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D411-4. DOI:10.1093/nar/gkj141 | PubMed ID:16381900 
+
+Peri S, Navarro JD, Kristiansen TZ, Amanchy R, Surendranath V, Muthusamy B, Gandhi TK, Chandrika KN, Deshpande N, Suresh S, Rashmi BP, Shanker K, Padma N, Niranjan V, Harsha HC, Talreja N, Vrushabendra BM, Ramya MA, Yatish AJ, Joy M, Shivashankar HN, Kavitha MP, Menezes M, Choudhury DR, Ghosh N, Saravana R, Chandran S, Mohan S, Jonnalagadda CK, Prasad CK, Kumar-Sinha C, Deshpande KS, and Pandey A. Human protein reference database as a discovery resource for proteomics. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D497-501. DOI:10.1093/nar/gkh070 | PubMed ID:14681466
+
+## IntAct
+
+PSI XML from IntAct has occasional errors, the fullName of the organism of some interacting proteins is absent when the shortLabel of the organism is 'in vitro', these are usually short peptides (fullName is used as a source of species information, thus Bio::Species objects can't be constructed). In one file I examined there were only a few proteins like this, they could be corrected by hand (BIO 18:16, 31 December 2005 (EST)).
+
+## MINT
+
+PSI XML from MINT has occasional errors, the fullName of the organism of some interacting proteins is absent. BIO 13:46, 2 October 2006 (EDT)
+
+Hermjakob H, Montecchi-Palazzi L, Bader G, Wojcik J, Salwinski L, Ceol A, Moore S, Orchard S, Sarkans U, von Mering C, Roechert B, Poux S, Jung E, Mersch H, Kersey P, Lappe M, Li Y, Zeng R, Rana D, Nikolski M, Husi H, Brun C, Shanker K, Grant SG, Sander C, Bork P, Zhu W, Pandey A, Brazma A, Jacq B, Vidal M, Sherman D, Legrain P, Cesareni G, Xenarios I, Eisenberg D, Steipe B, Hogue C, and Apweiler R. The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data. Nat Biotechnol. 2004 Feb;22(2):177-83. DOI:10.1038/nbt926 | PubMed ID:14755292 
+