The question at hand is how to most effectively take a query list (of over 100 entries) containing multiple different gene and/or protein identifiers and convert them all to the same type of identifier.
EDIT 1: I guess all I really need is a table/csv file with one protein on each line, and the different names for that protein in the columns. Then I can easily use a script to extract the information I need.
At the moment I have tried several different conversion websites (http://www.protocol-online.org/prot/Research_Tools/Online_Tools/Sequence_Analysis/Gene_ID_Conversion_Tools lists a few of the best ones), all of which requires the user to input the same type of ID (and to always know which type you have, making for a lot of manual work). And for several searches it ends up being a few that these websites can't determine, but which a search using UniProt can find. Therefore, the best way I have found to do this is to use the manual insertion of the search term into UniProt, and then take the best Homo sapiens match and map my query to this. The closest source have found that may hold an answer is http://www.uniprot.org/faq/28#batch_retrieval_of_entries although I am not sure if this is the best way to go about this.
My question is then how to best automate this using the command line (I have been given the impression that this is possible, but I have no idea as to how to go about doing this specific query).
Example querry list:
ACTB_HUMAN Ceruloplasmin (CF, F) Complement C1s subcomponent (F) Complement C3 (F) Complement C5 (F) Desmoplakina Haptoglobin-related protein (F) Hemopexin (CF) Inter-alpha-trypsin inhibitor heavy chain H1 (CF, F) Lactotransferrin Phosphatidylinositol-glycan-specific phospholipase Da Plasminogen (F) Protein AMBP Serum albumin Vitamin K-dependent protein S (F) ARHL1_HUMAN AFAM_HUMAN A1AT_HUMAN ANXA1_HUMAN ANXA5_HUMAN APOA1_HUMAN
example output for first two (input - output (UniProt ID)):
ACTB_HUMAN P60709 Ceruloplasmin P00450