I used Gene and protein tag cloud workflow (http://tech.knime.org/gene-and-protein-tag-cloud-example) but I realized that not all proteins which were tagged by Abner were in the cloud and they have a tag (Protein[Abner]) which was not in the POS filter and I don't know if I can edit the POS tagger list or I can use any other node which can collect all those words which were tagged by Abner. I will appreciate your reply.
terms, tagged by named entity tagger such as e.g. ABNER tagger (but not POS tagger) are set "unmofifiable" by default. This means they will not be filtered or modified by any preprocessing node used afterwards. If the "unmodifiable" flag ist not set (see filter and node dialog) the flag ist not set or ignored.
To filter terms tagged by the ABNER tagger you can use the "ABNER Filter" and specify which terms e.g. Proteins or Genes are filtered and which not.
In General: Each tagger has a tag set by which terms are tagged and for each tag set there exists a filter. The POS Filter filters terms only based on POS tag sets, the ABNER Filter based on ABNER tag set and so on.