This is a putative overall requirements list for the Open Tree of Life project, focused on software competence. It is intended to complement, not replace, the Trello board, which is for short term planning and to act as a wish list.


This list is meant as a management and planning tool. Possible uses:

1. Help set priorities as we plan work, and manage triage as we run out of time. Activities not directed toward meeting requirements should be given lower priority than those that do.
2. Assist architectural design decisions. Designs need to accommodate items on the requirements list, and needn't deal with things not on the list.

This list will be filled in by JAR as he continues to learn about the project.

Key:

• Defender = PI who has raised this to level of requirement; and can provide details, rationale, etc.
• How to test = what to do, operationally, to see whether requirement is met / figure out whether we're done
• URI(s) = source of commitment, or further information about commitment
• Reason = why this is so important that the defender thinks this is a requirement
• Importance = deal breaker, must, [really] should
• Urgency is by phase (I = summer 2013, II = spring 2014, III = spring 2015)
• Consensus = who else supports / disagrees with this as a requirement

Defender	Short description	How to test	URI(s)	Reason	Importance (must/should)	Urgency / phase	Notes	Consensus
SS	Generate a tree of life	Comprehensive, connected, and no cycles?		Main point of project	Deal breaker	I
KC	Browse draft tree/graph	At web site, can find tree easily, see all of it? Bare minimum would be NCBI-like	FAQ		Deal breaker	I
KC	Download entire draft tree/graph	Working hyperlink(s) to file(s) in some format that anyone can download?	Collaborators	Essential service	Deal breaker	I	EOL acceptance would be nice
KC	Extract subtree / subgraph via UI	Is subtree induced by given leaf set visible/extractable by non-programmers? (minimal: Newick string or NEXML given list in textarea)		Community need	Must	I	phylotastic
KC	Extract subtree / subgraph via API	Can get/use subtrees using R (or equivalent language)? Do we show up on ROpen's list of data packages?		Community need	Must	I?	e.g. ROpen
KC	Provenance drill-down	For any node or edge, can easily find supporting trees/data/taxonomies/synthesis methods (in UI, API, and dump)?		Transparency	Must	I
KC	Synthesis tool	Synthesis tool/service - offline	FAQ, summary	Service	Must	I
	Community contributions	High latency (manual / reviewed) input to opentree		Growth		I
KC	Track changes to external taxonomies	Are recent additions to NCBI, union4, CoL, etc. reflected in opentree with a latency 6 months?		Freshness, credibility	Must	I
JR	Attribution	Is information attributed to its source per academic community standards?		Right Thing	Must to extent reasonable	I	potential problems around specificty and attribution stacking
	Enable reproducibility	Keep a sequence of old versions of the graph and synthetic tree, and query software, for citation purposes (but not of the synthesis methods?)		Reproducibility		I?	but community standards around reproducibility are low
KC	Pull from Dryad	Do new phylogenies+data sets entered via Dryad show up (following request initiated in Dryad)?	Collaborators	NESCent	?	I?
KC	Push to Dryad	Do data+phylogeny entered in opentree show up in Dryad (on request from opentree)?	Collaborators	NESCent	?	I?	Risky to delay this one. Solves embargo issue
SS	Level of support within source tree	Is level of support available (in UI, API, dump)?				II?	bootstrap
SS	Level of conflict between source trees	Can distinguish agreed parts of graph / draft tree from conflict-ridden (in UI, API, and dump)?	proposal	Transparency	Must	II?
	User interface for phylogeny ingest	Low-latency update of the total tree by biologists		Scalability		II+
KC	Annotation database	Can add annotations to an annot. layer, and see? Can select annotation layers?	proposal	Utility(?)		II?	google earth, phyloreferencing
	Auto-track changes to external taxonomies	Automatic tracking of NCBI, union4, etc.? (Latency <2 days)		Freshness, credibility		III?
MH	Automatic update of gene tree estimates	(??) Does the system watch for new gene data from Genbank, re-run analyses when changes come in, and make the results available in the system?	home page, proposal	Scaling	Must	II
MH	Version control	Can a non-programmer update one of the source trees? Are preceding versions of source trees kept for comparison purposes?	proposal	Utility	Really should	III?	git	need clarity around purpose
?
	Push to Treebase	Does an uploaded phylogeny also show up in Treebase (on request from OToL)?	summary		Nice to have	II?	depends on help from treebase personnel	?
RR	Synthesize trees	Can a user vary tree generation parameters, such as priorities of methods or sources, to get different trees over the same tips?	proposal			II+		?
RR	Tree drawing tool	SVG-based phylogenetic tree illustration tool to help systematists prepare figures for print publication	proposal		Independent project	II		?
RR	Taxonomy of life	Feed phylogenies back to taxonomy, to generate improved overall hypothetical tree (taxonomy) of life	see here			II+		?
DS	Coordinate with PLoS Current ToL	[acceptance test for this feature?]			Nice to have	II+		?

(JAR's thoughts on possible requirements: offsite backups (still alive after fire in any single location?); longevity (still running 5 years post grant period?))