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meeting notes from 15 July 2008

Discussion of research questions

• flow from data to encoding
• encoding not necessary to do naive (automatable) analysis, e.g., parsimony with no special assumptions
• furthermore, encoding does not necessarily improve unsupervised analysis-- this would only be the case if the unsupervised analysis incorporates decisions based on the semantics of the encoding. For instance, we can have a column of data with 5 observed discrete states but no semantics. This might be an aligned nucleotide column with states A, T, C, G, and "-" (gap), or it might be a discrete morphological character with 5 states. However, this doesn't matter unless we can see the semantics that say "this is a nucleotide character" AND we can respond appropriately, e.g., by using a set of assumptions customized for nucleotides, e.g., ignore gaps and use transversion parsimony.
• single-char questions
  • what is the universe of possible states (disjoint classes in the state class)
  • what are the rules for state transformation, e.g.,
    • in the case of an "absent" state?
    • in other cases?
• pair-of-char questions
  • coordinated behavior
  • prior odds of correlation -- if we can estimate this, we have more statistical power to detect correlations
    • one measure for chars on cells A and B is rank(common_ancestor(A,B)) considering the cell lineage tree
    • another measure is physical proximity
• big evo-devo type questions
  • the two above measures of prior odds of correlation address two different modes of developmental effects
    • inheritance of an internal state (cyoplasmic determinants)
    • response to an external signal (induction)
  • so, we might be able to address this distinction-- which of the two is more important
  • find shortest path between A and B including both common ancestors and common locations, e.g., the link between A and B could be that their grand-mothers (inherited info) were adjacent (proximity info)
  • can we predict unknown inductions in development by examining character correlations?
  • are nematodes really more "mosaic" than sea urchins, etc

char 9: participation of innermost progeny of P(4,8).p in vulva

chars 10 to 12: Competence_of_P3.p (or P4 or P8) _to_adopt_vulva_fate

• this applies under an abnormal condition of ablation
  • ablation of some { P5.p, P6.p, P7.p }
  • ablation in developmental stage early L4
• but since P3.p, P4.p and P8.p undergo PCD in some TUs, they cannot be ablated

char 13: size of competence group

• count of cells in a certain stage (what stage?) whose lineage ends with state
• this character is a derivative of chars 10 to 12

chars 19 to 21: induction characters

• this is based on anchor cell ablation.
  • In elegans: ablate before critical time, no vulva; ablate after critical time, normal vulva.
  • In pristionchus, its not just anchor cell inducing the change, its "several cells of the somatic gonad" (p. 1927) in L4: ablating this very early, no vulva; ablating intermediate time, all cells reach secondary fate (vulval ring) but no primary fate (vulval opening); ablate late, everything normal
• see the paper by Haag and True, 2007, Curr. Biol. 17: R172-174

meeting notes from late May and June, 2008

Missed most of the Tuesdays in this period due to travel. Eric and Arlin met once for a rather informal discussion of results and PowerPoint^? presentation.

meeting notes from 13 May 2008

chars 2 to 8: individualized fates of P3.p to p9.p or their descendants

• in the worm_anatomy ontology, this is a character in the Cell domain
• the observed states can be mapped to existing anatomy terms!!
  • 'PCD' in Kiontke corresponds to 'apoptotic cell' in ontology
  • 'epidermal' in Kiontke corresponds to 'hypodermus' in ontology
  • 'vulval' in Kiontke corresponds to 'vulval cell' in ontology

At this meeting we tried to create some instance data:

• TUs Panagrellus redivivus, Caenorhabditis elegans, C. briggsae and Pristionchus pacificus
• character P4.p_fate
• character_state_datum belonging to this and belonging to a species
• it seems that I can't use has_state to give character_state_datum the state from an abstract class

meeting notes from 6 May 2008

chars 22 to 27: division patterns of P6.p and some other cells or symmetry-related pairs of cells (6 May meeting)

• these are the four granddaughters
• we know who they are: P6.paa, P6.pap, P6.ppa, P6.ppp
• the states represent the division pattern like TTTT TUUT and so on
• note that this is a compound character
  • four atomic characters, in order
  • compound states are sequences of atomic states
  • atomic states are T = transverse, U = undivided, L = longitudinal, O = oblique (to T and L)
• how to express atomic state U
• how to express atomic state T, L, O
  • if the other species were like this, we could just refer to the spatial relationships of daughter cells, but this won't work because we are using only the C. elegans ontology; in C. elegans they all divide transversely, so the great-grand-daughters are <grand-daughter>l and <grand-daughter>r; we can't name these cells in other species because they have different names
  • we could introduce a division concept. it could have an orientation or plane of division.
    • class division
    • property reproduces_by
    • property born_by
    • property occurs_during
    • property has_axis_of_division
    • class orientation
    • subclass direction
    • data property has_anterosinistral_angle
    • data property has_anterodorsal_angle
    • data property has_positive_radial_coordinate

meeting notes from 29 April 2008

* char 16, larval stage at which Z1 and Z4 divide

• states are L1, L2, L1 and L2 (polymorphism), and L1 or L2 (uncertainty)
• in worm_development ontology
  • L1 is WBls_0000024
  • L2 is WBls_0000027
  • Now, we can create an instance and assign it to the L1 class. What should the instance be?
    • the instance is state_0_of_char_16. This can't be right because there are many instances of this state.
    • the instance is state_of_char_16_in_C_elegans. This is ok. We need 51 instances of the state of this character, for each of the 51 OTUs.
• what does "Z1 and Z4 divide" mean? Its NOT the division of Z1 and Z4 from a common ancestor, but the coordinated division of Z1 and Z4 into their daughters (Z1.a and Z1.p, Z4.a and Z4.p). Z1 and Z4 are developmentally symmetrical. See http://www.wormatlas.org/Postemblingonad_1979/results.html
• so, we need to create a property of "divides_during_stage" with domain = cell and range = stage.
• then, we need to create an elegans instance ?? in which the Z1 and Z4 instances have the property "divides_during_stage" L1 or L2.

meeting notes from 22 April 2008

char 1, number of Pn.p cells

• does not vary in the species examined (always 12), so we could ignore this if we want
• PN.p cells all descend from the embryonic AB.prap lineage; pcd = programmed cell death, important scientific result showing that same signal could lead to epi fate in one case, pcd in another
• we could specify this with something like cardinality of (descendant_of Pn.p and has_stage Lx and has_location ventral_midline)
  • the has_stage Lx part is necessary so that we don't count descendants in the wrong larval stage-- we want to count only in the stage where the Pn.p configuration is counted. I don't know what this stage is, exactly.
  • another way to do the above is to limit the generation.

Notes on coding of characters

1	Number_of_Pn.p_cells	lineage concept suffices?	{ twelve other_than_twelve }	integer (data property)
2	P3.p_fate	lineage concept suffices?	{ epidermal PCD }	'C elegans cell and anatomy ontology':'Cell':{epithelial cell} (PCD?)
3	P4.p_fate	lineage concept suffices?	{ epidermal PCD vulval }	{epithelial cell, vulval cell} (PCD?)
4	P5.p_fate	lineage concept suffices?	{ epidermal PCD vulval }	{epithelial cell, vulval cell} (PCD?)
5	P6.p_fate	lineage concept suffices?	{ epidermal PCD vulval }	{epithelial cell, vulval cell} (PCD?)
6	P7.p_fate	lineage concept suffices?	{ epidermal PCD vulval }	{epithelial cell, vulval cell} (PCD?)
7	P8.p_fate	lineage concept suffices?	{ epidermal PCD vulval }	{epithelial cell, vulval cell} (PCD?)
8	P9.p_fate	lineage concept suffices?	{ epidermal PCD vulval }	{epithelial cell, vulval cell} (PCD?)
9	participation of innermost progeny of P(4,8).p in vulva	descendant_of P4.p and location_in vulva	{ none both P8.p_only }	{ list of cells, restricted by parentage }
10	Competence_of_P3.p_to_adopt_vulva_fate	onto_interp	{ not_competent competent PCD }	{ binary with "PCD" }
11	Competence of P4.p to adopt vulva fate	onto_interp	{ not_competent competent }	binary (data property)
12	Competence of P8.p to adopt vulva fate	onto_interp	{ not_competent competent }	binary (data property)
13	size_of_competence_group	onto_interp	{ 6_cells 5_cells 4_cells 3_cells more_than_6_cells }	integer
14	Posterior migration of midbody Pn.p cells	onto_interp	{ no yes }	binary (data property)
15	vulva_center	onto_interp	{ in_P6.p between_P6.p_and_P7.p in_P6.p_but_asymmetric }	{ compound: symmetry plus location relative to coordinate system; location qualifiers "in", "between" etc refer to Cells }
16	Z1_and_Z4_divide_during	onto_interp	{ L1 L2 }	{ development ontology: larval stages}
17	Ovary_number	onto_interp	{ 'two_(didelphic)' 'one_(monodelphic)' }	integer (data property)
18	DTC_migration_pattern	onto_interp	{ 'out,_dorsal,_back' 'out,_dorsal,_back,_ventral' 'out,_dorsal,_back,_ventral,_second_turn' }	{ sequence_of something to do with axis directions}
19	Dependence on gonadal induction before VPCs divide	onto_interp	{ no_gonad_requirement dependent_on_gonad }	binary (data property)
20	P6.p requirement for late induction	onto_interp	{ not_required required '(not_applicable)' }	ternary (data property)
21	Source of first induction signal	onto_interp	{ gonad AC gonad_independent }	{ huh? }
22	P6.p_lineage_pattern	onto_interp	{ TTTT TUUT UTTU UUTT UTTT }	sequence_of(4) e in { U, T }
23	'P (5,7).p lineage pattern'	onto_interp	{ UUUU LUUU LLUU LLLU LLTU LULU LOTU sUUU UULL }	sequence_of(4) e in { U, T, L, s, O }
24	'A: P5.paa/P7.ppp division'	onto_interp	{ U L T O }	{ onto_interp . . . }
25	'B: P5.pap/P7.ppa division'	onto_interp	{ U L T O }	{ onto_interp . . . }
26	'C: P5.ppa/P7.pap division'	onto_interp	{ U L T }	{ onto_interp . . . }
27	'D: P5.ppp/P7.paa division'	onto_interp	{ U L T }	{ onto_interp . . . }
28	P4.p_lineage_pattern	onto_interp	{ 'S_(no_division)' 'SS_(1_division)' 'Sss_(2_divisions;_inner_daughter_divides_again)' 'SSSS_(3_divisions)' '(SSLL)_(5_divisions;_inner_granddaughters_divide_L)' 'LLLL_(7_divisions;_8_cells)' }	{ sequence of division events restricted by cell lineage and stage}
29	P8.p_lineage_pattern	onto_interp	{ 'S_(no_division)' 'SS_(1_division)' 'ssS_(2_divisions)' 'SSSS_(3_divisions)' 'LLSS_(5_divisions)' 'LLLL_(7_divisions)' }	{ sequence of division events restricted by cell lineage }
30	P3.p_division_frequency	onto_interp	{ in_less_than_20%_of_cells more_than_20%_of_cells PCD }	float_range
31	relative_chronology_of_P6.p	onto_interp	{ inner_granddaughter_cells_divide_first outer_granddaughter_cells_divide_first not_applicable }	{ sequence_of ? }
32	number of P(5,7).p division rounds at L3 to 4 molt	onto_interp	{ none one two two_or_three three }	list_of integer
33	number of P6.p division rounds at L3 to 4 molt	onto_interp	{ none one two two_and_three three }	list_of integer
34	vulva formed of a stack of rings	onto_interp	{ yes no }	binary (data property)
35	# rings by A granddaughter pairs	onto_interp	{ one two none }	integer (data property)
36	# rings by B granddaughter pairs	onto_interp	{ one two }	integer (data property)
37	# rings by C granddaughter pairs	onto_interp	{ one two }	integer (data property)
38	# rings by D granddaughter pairs	onto_interp	{ one two }	integer (data property)
39	# rings by E granddaughter pairs	onto_interp	{ one two }	integer (data property)
40	# rings by F granddaughter pairs	onto_interp	{ one two }	integer (data property)
41	A1_fuses	onto_interp	{ with_epidermis with_A2 A_fuses_with_epidermis }	{ onto_interp . . . }
42	A ring longitudinal fusion	onto_interp	{ no yes }	binary (data property)
43	B ring longitudinal fusion	onto_interp	{ no yes }	binary (data property)
44	B ring transverse fusion	onto_interp	{ no yes }	binary (data property)
45	C ring longitudinal fusion	onto_interp	{ no yes }	binary (data property)
46	C ring transverse fusion	onto_interp	{ no yes }	binary (data property)
47	D ring longitudinal fusion	onto_interp	{ no yes }	binary (data property)
48	E ring longitudinal fusion	onto_interp	{ no yes }	binary (data property)
49	E ring transverse fusion	onto_interp	{ no yes }	binary (data property)
50	F ring longitudial fusion	onto_interp	{ no yes }	binary (data property)
51	F ring transverse fusion	onto_interp	{ no yes }	binary (data property)
52	total number of rings predicted	onto_interp	{ five six seven eight }	integer (data property)
53	shape_of_vulva	onto_interp	{ slit pore }	{ onto_interp . . . }
54	vulva_position	onto_interp	{ midbody slighly_posterior_of_midbody far_posterior_of_midbody }	{ onto_interp . . . }
55	Vulva_anterior_tilt	onto_interp	{ no yes }	binary (data property)

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