Perhaps this will help you. Without more text it is a bit difficukt to explain the relationship precisely. The text following "especially since" gives a background/point of reasoning for the opinion expressed in the first part of the sentence.

several opportunities (subject) dealt with issues (predicate)

The predicate can easily be missed since the semicolon is misplaced (i.e., misleadingly suggests a closure).
Apart from that, the sentence looks more or less clear to me.

WIPO contributed to the work of organizations and worked out how that contribution could be done; especially
since several opportunities had opened the way to deal with issues such as technology transfer, where IP rights played a key role.

I'll try to rephrase the content of this sentence in very simple words:

The important thing was not so much the fact *that* WIPO contributed .... but *how and what* WIPO contributed.

Explanation:
Several times when people attempted to address issues like climate change, public health, food security, and processes such as RIO+20, the discussion focused on issues such as technology transfer, fan area where IP rights play a key role.

This sentence structure is confusing because
1) at one point in the list a semicolon is used instead of a comma (as Gert has already pointed out);
2) there is a noun-verb mismatch:
"... several opportunities to open issues [..... ] dealt with issues [....]".
(Do opportunities deal with things? I don't think so.)

Hope this helps.

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Note added at 3 hrs (2012-01-23 23:35:21 GMT)
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correction: not "fan area" but "an area" :-))