Add SOP docs for all uPheno social workflows

docs/howto/reconciliation.md

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+## The uPheno reconciliation workflow: Standard Operating Procedures
+
+
+The reconciliation workflow is devided in the following subproblems:
+
+
+1. Patternisation: The process of defining patterns for groups of related phenotypes, such as "abnormal morphology of anatomical entity". The goal is to increase
+   coverage of EQs that correspond to uPheno patterns.
+1. Pattern review: The process of reviewing pattern instances (usually in a spreadsheet) and determine if 
+   (a) the pattern used for defining the phenotype is apropriate and
+   (b) the fillers used for defining the phenotypes are appropriate
+   (c) the inferences facilitated by a pattern are appropriate
+   The goal of pattern review is to determine if EQs that correspond to uPheno patterns are appropriate for a given phenotype.
+1. Pattern reconciliation: The process of ensuring that two different groups defining an _analogous_ phenotype are using (a) the same pattern and (b) the same or analogous fillers.
+
+In this document, we will describe how each of these are executed in practice (standard operating procedures).
+
+
+### Patternisation
+
+Patternisation is the process of defining patterns for groups of related phenotypes, ...
+
+There are two separate SOPs, one for new terms, and one for retrofitting defined phenotypes with EQs with a formal pattern.
+
+**SOP: New Terms**:
+
+- When a new term is added, the corresponding EQ logical definition should only be defined if a pattern exist. The curator checks the uPheno pattern library.
+  Only if no suitable pattern is found, the curator can proceed to defining a new pattern (see SOP "Add new pattern to uPheno pattern library" below).
+
+**SOP: Create patterns for existing EQs
+
+- Match using a generic pattern
+- What to do if EQ differs widely
+
+**SOP: Add new pattern to uPheno pattern library**
+
+- A new pattern is suggested on an issue tracker.
+- A pull request is created proposing the new pattern.
+- ....
+
+### Pattern review
+
+The process of reviewing pattern instances (usually in a spreadsheet) and determine if 
+ (a) the pattern used for defining the phenotype is apropriate and
+ (b) the fillers used for defining the phenotypes are appropriate
+ (c) the inferences facilitated by a pattern are appropriate (this can be seen as a sub-problem of (b))
+ The goal of pattern review is to determine if EQs that correspond to uPheno patterns are appropriate for a given phenotype.
+
+**SOP:**
+
+- Describe the workflow you have been running with MP
+
+### Pattern reconciliation
+
+The process of ensuring that two different groups defining an _analogous_ phenotype are using (a) the same pattern and (b) the same or analogous fillers. 
+This includes the case where 1 ontology has an EQ, and the other does not.
+
+**SOP:**
+
+- Describe here all your ideas for this process, and how you currently do it with MP (Sue, Anna) and HP (Leigh).