Difference between revisions of "POC Conf. Call 7-19-11"

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In attendance:  
 
In attendance:  
  
−
POC members:  
+
POC members: ''Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Barry Smith (University at Buffalo, NY), Justin Elsner (OSU), Justin Preece (OSU)''
−
Absent:  
+
 
−
+
Absent:'' Chris Mungall (Lawrence Berkeley National Lab), Dennis Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell University)''
 +
 
 
Collaborators: none
 
Collaborators: none
  
 +
Acceptance of the minutes from the [[POC_Conf._Call_7-12-11]]?  ''There were no changes, additions, or deletions.''
 +
 +
 +
=Tech Talk=
 +
==A web service for PO terms==
 +
 +
Justin Preece will demonstrate a prototype web service providing PO terms from the AmiGO database. This was originally built for his annotation wiki project, but could be expanded for general use and advertised as POC "technical outreach", to be consumed by other people's applications wanting to use PO data.
 +
 +
'''Example screenshots'''
 +
* [[Media:PO_term_web_service_autocomplete.png|PO term autocompletion in raw JSON format]]
 +
* [[Media:PO_term_web_service_term_detail.png|Term detail in raw JSON format]]
 +
* [[Media:PO_term_web_service_usage_autocomplete.png|Autocompletion, as used by another web application (outside of plantontology.org)]]
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* [[Media:PO_term_web_service_usage_term_detail.png|Term details, retrieved and used by another web application]]
 +
 +
JP and JE propose to add such a web service to plantontology.org.
 +
 +
For those interested in some technical background info: see Wikipedia's entries for [http://en.wikipedia.org/wiki/Web_service web service], [http://en.wikipedia.org/wiki/Representational_State_Transfer#RESTful_web_services RESTful web services], and [http://en.wikipedia.org/wiki/JSON JSON].
 +
 +
 +
''JP: Purpose of these web services would include: data accessibility, potential to increase exposure of the PO to more users and application, technical outreach tool development'' 
 +
 +
Questions: Do the keyword searches include synonyms?  That should be possible if the terms are in the database''
 +
 +
''What about alternate spellings? add the British spellings in the synonym filed''
 +
 +
''Talk with the other groups at ICBO about how they deal with this issue.''
 +
 +
''Comments: BS shared a link with us to a  [http://ucsdbiolit.codeplex.com/ Microsoft Word plugin] that will give you a drop down list of terms from ontologies when you are writing a paper.''
 +
 +
==Update on the Translations:==
 +
 +
details TBA...
 +
 +
''JE has tested script for Japanese terms. Some problems putting them in alphabetical order, because it doesn't recognize UTF8 characters. Should work okay as long as there is only one synonym for each term (which is the case for Japanese synonyms).''
 +
 +
=Letter for OBO-Foundry acceptance=
 +
 +
-PJ sent around a draft letter outlining the PO request for review:
 +
 +
Comments from BS:
 +
 +
* ''Should go through list of OBO Foundry criteria. Order the points in the letter as the same order as the criteria.''
 +
* ''Most important is proving a '''multiplicity of independent users'''. Not a problem for PO, but needs to be included.''
 +
* ''Also should mention that PO is supporting tool development. Not in the OBO Foundry criteria, but will impress reviewers with good citizenship.''
 +
* ''Need to make the discussion of the relations consistent- derives_from an experimental manipulations''
 +
 +
 +
See the associated page that LC created to gather the information for the OBO review : [[OBO_Foundry]]
 +
 +
=Plant Physiology Publication=
 +
 +
Comment on relations from BS (re. the letter and the paper): ''In RO, derives_from does not refer to manipulated material, but PO manuscript describes it that way. We should have a more specific relation for this. Need to see what others are using. Check with OBI.''
 +
 +
 +
RW:''We have only been using develops_from for in vitro structures, but we did not necessarily mean to define it in terms of manipulations.''
 +
 +
''We reviewed the differences between transformation and derivation.  Transformation is always one to one. Deriviation always involves a fusion or a fission.  Classic example of transformation is zygote to embryo to child to adult. Example of derivation is zygote from egg cell and sperm cell.''
 +
 +
''Develops_from can be use when we don't know or don't want to specify if there is a transformation or derivation.  This is not necessarily recommended, except that people really want to use it.''
 +
 +
''Transformation_of is a little vague, because there are underlying derivations that happen during a transformation (to the parts of the thing that is transforming). For this reason, develops_from might be better to use.''
 +
 +
''Talked about adding a new relation called "experimentally_derived_from" or maybe better "derived_from_by_manipulation.''
 +
 +
'''''Action items:'''''
 +
 +
-Check with OBI to find out if they have a relation similar to what we need for in vitro structure.
 +
 +
-Rework the manuscript re. develops_from and derives_from so that is consistent with what we are doing.
 +
 +
-Be sure descriptions of relations in the OBO Foundry letter are consistent with the manuscript, and that all are accurate.
 +
 +
 +
''see additional notes in text below''
 +
 +
=Issues from last week's discussion=
 +
==Use of ''develops_from'' and ''derives_from'' relations in PO==
 +
 +
Last week we discussed how ''develops_from'' can be used to mean either ''transformation_of'' or ''derives_from''.
 +
 +
From RO:
 +
 +
'''transformation_of:''' Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation.
 +
 +
And: ...one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes.
 +
 +
'''derives_from:''' Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later.
 +
 +
And: ...from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t.
 +
 +
 +
From http://www.berkeleybop.org/ontologies/obo-all/ro_proposed/ro_proposed.obo
 +
 +
id: OBO_REL:develops_from
 +
 +
alt_id: OBO_REL:0000038
 +
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name: develops_from
 +
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def: "A relation between two continuants, C and D. C develops_from D if C derived_from D or C transformation_of D. On the class level: C develops from D if and only if, for any x and any time t, the following holds: if x instantiates C at time t, then 1. either for some time t1, x instantiates D at t1 and t1 precedes t, and there is no time interval t2 such that x instantiates C at t2 and x instantiates D at t2 ; 2. or for some time t1 , there is some y such that y instantiates D at t1 and x derived_from y. On the instance level: x develops_from y is indistinguishable from x derives_from y" [GOC:cjm]
 +
 +
comment: Examples: eye develops_from eye disc; erythrocyte develops_from reticulocyte. Note that ontologies should use either derives_from or transformation_of where appropriate, but the develops_from relation can be used where one does not want to differentiate between these 2 cases
 +
 +
is_transitive: true
 +
 +
! domain: snap:IndependentContinuant
 +
 +
! range: snap:IndependentContinuant
  
−
Acceptance of the minutes from the [[POC_Conf._Call_7-12-11]]?
 
  
−
=User requests, Plant Anatomy Ontology:=
+
We decided we needed to examine the instances of each of these relation in the PO on a case by case basis.
  
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==TraitNet requests:==
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====derives_from relations in PO:====
  
−
===[https://sourceforge.net/tracker/?func=detail&aid=3080911&group_id=76834&atid=835555 podarium]===
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lateral root primordium (PO:0000016) derives_from pericycle (PO:0006203) '''''This one should be develops_from'''''
  
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Their comment: is synonym to tubercle (but it isn't exactly the same)
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leaf-derived cultured plant cell (PO:0000007) derives_from leaf (PO:0025034)
  
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podarium (from Beentje 2010): (in cacti or other succulents) a modified leaf base functioning as the photosynthesising organ.
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root-derived cultured plant cell (PO:0000008) derives_from root (PO:0009005)
  
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tubercle (from Beentje 2010): (in ball- or barrel- shaped cacti), cone-shaped protuberances that are enlarged modified leaf bases fused with adjacent stem tissue (tubercle has two other definitions as well).
+
''change the latter two to something like derives_by_manipulation_from''
  
−
[[http://docs.google.com/viewer?a=v&q=cache:NuEGm3IiDYAJ:www.fcla.edu/FlaEnt/fe84p474.pdf+cactus+morphology&hl=en&gl=us&pid=bl&srcid=ADGEEShKIXm284nTEhC69_8ZMUsUqJCxZF-KpqW7C_7nqrap5cB6PoZqgFe_R19AFvRD7j59jql-ugEv-Dfv0aNgJ1RcHunV0oxR67OB_e9iY4b1hBRqkXBK29vi3NYbon9rCkAm2fRR&sig=AHIEtbRWmPk6sb2L0_VDc_CoSY2U8RRYjA This article]] describes podaria and tubercles (as synonyms) as a swelling of the stem (cladode) fused with the base of a leaf:
+
====develops_from relations in the PO:====
  
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"Tubercles (or podaria) are swellings below the conic leaves of the pad (long-shoot). The upper part of the conic leaf is the blade, which abscises in a week or two at a notch. The leaf base, or petiole, and adjacent stem tissues are fused together forming the tubercle. The tubercle may elongate and swell such as in species of pincushion cacti (Mammillaria spp.). If the raised tubercles align vertically around the stem they can coalesce with those directly above and below forming ribs, like those of the saguaro."
+
See [[list of develops_from relation in PO 07-2011]]
  
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'''proposed def. podarium or tubercle:''' ''under construction''
+
===''participates_in'' relation===
  
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==[https://sourceforge.net/tracker/?func=detail&aid=3040048&group_id=76834&atid=835555 Legume terms] submitted by Austin Mast==
+
We use the participates_in relation to describe the whole plant growth phase in which an anatomical entity occurs. For example:
  
−
Remaining:
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sporangium ''participates_in'' sporophyte phase.
  
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===[https://sourceforge.net/tracker/?func=detail&aid=3165984&group_id=76834&atid=835555 phyllode]===
+
There is no restriction on the ''participates_in'' relation that says that just because A ''participates_in'' B, it cannot also participate in C.  
  
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Last week, we looked at examples of leaves where the petiole has phyllode development, but there is normal lamina development (with leaflets) beyond the petiole. We need a term to describe this, as well as when the whole leaf develops as a phyllode.  
+
Saying sporangium ''participates_in'' sporophyte phase does not preclude the possibility of sporangium ''participates_in'' gametophyte phase (although of course it doesn't).  
  
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====Background:====
+
What we really want to say is sporangium ''participates_in_only'' sporophyte phase. Should we create a more specific relation to say this? This would be much more powerful for reasoning than the regular ''participates_in'' relation.
  
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Boke 1940 (http://www.jstor.org/stable/2436690, DOI:10.2307/2436690) uses the term phyllode to refer only to those leaves without leaflets:  
+
From CM (via email):
  
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"The seedling usually displays 1 even-pinnate leaf, 1 bipinnate leaf, and several transition forms. Pinnate leaves and transition forms possess an apical pointlet like that of the phyllode."
+
adding the only qualifier is easy in OWL, but not in OboEdit. Also, although we want to exclude structures from participating in other whole plant growth stages, we don't want to exclude them from participating in other processes (which the only qualifier would do).
  
 +
In OWL, we cold say: sporangium SubClassOf participates_in only ('sporophyte phase' or not 'life cycle stage'
  
−
The main reference people cite for phyllodes is: '''D.R. Kaplan 1980''', Heteroblastic leaf development in Acacia: morphological and morphogenetic implications, La Cellule 73, pp. 137–203.
+
but this is difficult in OboEdit.
  
−
Kaplan say: "The present developmental comparisons between phyllodes and pinnatifid leaves in seedlings of Acacia have demonstrated unequivically that the blade of the phyllode is the longitudinal positional homologue of the lamina of the fully pinnate leaf, at all stages of development. At no stage is the phyllode blade merely a petiolar derivative, nor is there evidence of lamina suppression in favor of petiolar elaboration as suggested in the classical developmental paradigm."
+
Chris recommends that we:
  
 +
i. Create a shortcut relation called (OK, we need a better name here!) "participationally_disjoint_from".
  
−
'''Some more contemporary uses of the term phyllode:'''
+
ii. Add a macro expansion definition to this
 +
(tech. spec. is here: http://oboformat.googlecode.com/svn/trunk/doc/obo-syntax.html#7  -- but I can do this for you)
  
−
'''Gardner et al. 2005''' (http://www.publish.csiro.au/view/journals/dsp_journal_fulltext.cfm?nid=150&f=SB04052):
+
iii. Make direct triples between sporophyte and gametophyte in OE using this relation (note this is not an all-some relationship, it's a direct relationship at the class level. confused yet?)
  
−
"A phyllode usually consists of a pulvinus and photosynthetic region, although it can be sessile, decurrent with the stem, or reduced to scales. The photosynthetic region is highly variable and ranges from vertically flattened, through terete, quadrangular and triquetrous to horizontally flattened. Phyllodes usually possess at least one extra-floral nectary on the adaxial nerve, and sometimes up to five. Boughton (1981, 1985) observed three types of extra-floral nectaries. She also investigated the indumentum and found almost all species have two kinds of trichomes, one glandular and one non-glandular (Boughton 1989). According to Arber (1918), '''the chief anatomical feature by which phyllodes differ from true leaf laminae is the occurrence of two opposing series of vascular bundles'''."
+
which would be similar to creating an OWL axiom that says: (participates_in some sporophyte) DisjointWith (participates_in gametophyte)
  
−
and later in the paper:
 
  
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"Previous approaches, such as basic anatomy and inferences from the sequence of heteroblastic leaf development in acacias, have led researchers to state that the phyllode is homologous with the petiole of a bipinnate leaf (e.g. Mann 1894; Goebel 1905; Troll 1939), or with the petiole and rachis (e.g. Bentham 1875; Reinke 1897), and make comparisons with the monocotyledonous leaf. Investigating the developmental morphology of phyllodes, Kaplan (1980) proposed a new model: that the phyllode is actually the positional homologue of the lamina of a bipinnate leaf. In essence, this suggests that the phyllode is directly comparable to a simple leaf. Kaplan’s theory does not, however, address the issue of the opposing vascular bundles found in phyllodes.
+
''This proposal is okay to use tentatively, but we should not go into too much detail about the participates_in relation in the current manuscript, because our usage of it may change as we rework the PGDSO. We can describe it more in the next manuscript.''
  
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"The pattern of branching observed in the vascular bundles of A. verniciflua phyllodes suggests that the abaxial marginal nerve is homologous to the mid-rib in a simple leaf. This implies that laminar expansion occurs on both sides of the ‘mid-rib’, but vertically, and fused together. The emergence of the adaxial marginal nerve as two separate bundles, originating on opposing sides that eventually fuse rather than directly from the vascular ring found in the pulvinus, supports our interpretation and has been observed (together with other patterns) in several other Acacia species (von Wartburg 1991)."
+
''We still need to use or mention participates_in in the paper, in order to say how we would describe a gametophyte or sporophyte, but don't make it a focus.''
  
 +
''A sporophytes is a whole plant during the time it participates_in the sporophyte phase. We need a solution for this temporal issue.''
  
−
'''Leroy and Heuret 2007''' (doi:10.1016/j.crvi.2007.11.006): "The subgenera Phyllodineae... as the species are characterised by a polymorphism of vegetative characters where bi-pinnate leaves are replaced by '''a type of foliar organ''' called a phyllode."  and "...the different transitional forms range from pinnate leaves to phyllodes..." 
+
=Request from Cell Ontology (CL)=
  
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'''See fig. 1 in this paper.''' They refer a "flattened petiole" and a "flattened rachis" in transitional leaves.
+
CL plans to obsolete most of its plant cell types, and add xrefs to those for PO terms.
  
 +
CL will provide bridge files as part of the CL release process. An example of this is provided in the [http://icbo.buffalo.edu/2011/WorkshopB_Program.pdf WOMBO paper] (upcoming at IBCO).
  
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'''Yang et al. 2008''' (DOI: 10.1007/s11240-008-9424-7) use leaf as synonym for phyllode in Acacia. Refer specifically to phyllodes without any pinnate (sic) on top of them.
+
PO has appropriate terms for all but four of the CL terms, although two of the terms are obsolete (PO:0000373  mucilage cell and PO:0000020 starch sheath cell).
  
 +
==four problematic terms==
  
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'''Forster and Bonser 2009''', Annals of Botany, use the term phyllode to refer to adult leaves without leaflets: "Acacia implexa (Mimosaceae) is a heteroblastic species that develops compound (juvenile), transitional and phyllode (adult) leaves that differ dramatically in form and function."
+
PO does not have equivalent terms for these CL terms, because it was set up for only angiosperms. Suggest we add terms like these when we work on the revisions of conducting tissue and cells. The CL terms come form Esau's Anatomy of Seed Plants. For now, Terry has removed the problematic xrefs from CL, will update them if we add new terms.
  
 +
CL:0000399 phloem element (PO could add phloem element, similar to xylem element, parent to sieve element and phloem fiber)
  
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RW did not find any contemporary papers that said that a phyllode is a petiole.
+
CL:0000364 ray cell (PO has ray wood parenchyma, but ray cell could be parent to both ray wood parenchyma and ray tracheary element)
  
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Leaves that have phyllode-type development toward the base with leaflet development toward the tip are a type of transition leaf.
+
CL:0000294 sieve cell (could add this term for gymnosperms, if still used, see Esau)
  
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====Proposed terms and definitions:====
+
CL:0000268 sieve element (PO has sieve tube member, but sieve element could be parent to both sieve tube member and sieve cell)
  
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'''phyllode:''' An adult vascular leaf in which the laminar development is a median plane  (perpendicular to the axis), rather than the more common state of in a transverse plane (tangent to the axis). (ref: Lawrence)
+
''okay. we can contact them if we add terms for these.''
  
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Comment: Common in legumes of the genus Acacia. Lamina development in a phyllode occurs from activity of the abaxial meristem early in development, similar to unifacial leaves. Similar development occurs in some monocot leaves, but they are not called phyllodes. Transitional leaves also occur, in which the basal portion of the leaf develops similar to a phyllode, but the apical portion of the leaf develops normal leaflets (see PO:xxxxxxx, transitional phyllode-type leaf). In some leaves, the petiole may twist giving the appearance that the lamina is a phyllode, but it is not. Phyllodes are generally xeromorphic.
+
==epidermal cell==
 +
CM writes:
  
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is_a vascular leaf, is_a adult leaf
+
CL:0000362 ! epidermal cell [DEF: "An epithelial cell of the integument (the outer layer of an organism)."]
  
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Unifacial leaf as synonym? No- not the same, but similar development. See Kaplan 1970 (http://www.jstor.org/stable/2485311).  Might be better to make a parent term "ensiform leaf" which has children phyllode and unifacial leaf.
+
GO uses "epidermis" in this way. However, I would prefer something like:
  
 +
integumental cell (functionally defined, lives in CL or FUNCARO)
  
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'''phyllode-type transition leaf:''' A transitional vascular leaf in which the basal portion of the leaf has lamina development similar to a phyllode, and the apical portion of the leaf develops leaflets similar to a juvenile leaf.
+
epidermal cell (vertebrate sense, lives in CL)
  
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Comment: Common in seedlings of legumes of the genus Acacia.
+
plant epidermal cell (lives in PO with name "epidermal cell", imported into pan-euk view with obofoundry unique label "plant epidermal cell")
  
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===[https://sourceforge.net/tracker/?func=detail&aid=3165983&group_id=76834&atid=835555 bristle]===
 
  
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More complicated, because it is a phenotype term, and applies to structures other than stipules.
 
  
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Will discuss at a future meeting.
+
''PJ would prefer that they just take the PO branch for plant cells and import it into the CL.''
  
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=User requests: PGDSO:=
+
''They still need to obosolete (or merge) their terms, so there are not duplicates.''
−
==Maize GDB==
 
−
===[http://sourceforge.net/tracker/?func=detail&aid=3324056&group_id=76834&atid=835555 coleoptile emergence -- definition]===
 
  
−
From Mary at MaizeGDB: It would be more useful for maize if the definition for coleoptile emergence PO:0007045 were altered to be: Emergence of coleoptile from the seed (rather than above ground) . This could compare well to the radicle definition (PO:0007015 radicle emergence): The stage at which the radicle or root emerges from seed.  
+
''We confirmed our decision last week that epidermal cell should be renamed "plant epidermal cell"  When other ontologies import PO terms, they will have to remove "plant" from the name before appending "plant" to all of the PO term names.''
  
−
PO:0007045 cotyledon emergence is_a shoot emergence, and shoot emergence(PO:0007030) is defined as "Shoot or leaf breaks through soil surface."
+
''We need to talk to CL about how they will link to PO terms. Lol will see Terry Meehan at ICBO meeting, and/or we could set up a phone meeting with them.''
  
−
All of the sibling terms to cotyledon emergence (coleoptile, epidcotyl, and hypocotyl emergence) are also defined as when they break through the soil surface, so if we change one, we should change all of them.
+
=User requests, Plant Anatomy Ontology:=
 +
'''''postponed until a future meeting- see [[POC_Conf._Call_8-2-11]]'''''
  
−
'''Do we all agree that it is better to define terms relative to other plant structures instead of to the environment?'''
+
==[https://sourceforge.net/tracker/?func=detail&aid=3040048&group_id=76834&atid=835555 Legume terms] submitted by Austin Mast==
  
 +
===[https://sourceforge.net/tracker/?func=detail&aid=3165984&group_id=76834&atid=835555 phyllode]===
  
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PJ suggested that we don't need to obsolete and replace the terms, but RW feels that this is exactly the kind of change in definition that warrants obsoleteling the term and creating a new one.
+
==Maize GDB==
  
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Adding the replaced_by link would make moving existing annotations straightforward. There are 133 annotations on shoot emergence, including 1 from coleoptile emergence and 2 from cotyledon emergence.
+
===[http://sourceforge.net/tracker/?func=detail&aid=3324058&group_id=76834&atid=835555 transition leaf - definition]===
  
 +
===[http://sourceforge.net/tracker/?func=detail&aid=3356716&group_id=76834&atid=835555 leaf base]===
  
−
Also, '''all of these terms should be renamed as stages or phases''' rather than as developmental processes - so, for example, PO:0007045 should be called coleoptile emergence stage, rather than coleoptile emergence. The definitions should reflect the fact that they are stages, not processes.
+
===[http://sourceforge.net/tracker/?func=detail&aid=3357921&group_id=76834&atid=835555 style, silk, Poaceae style]===
  
−
Furthermore, shoot emergence is part_of seedling growth, but has no is_a parent, and seedling growth has no is_a parent. We should fix these while we're redefining the terms.
+
=Upcoming meetings 2011:=
  
 +
* '''International Botanical Congress (IBC2011)'''
  
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current structure:
+
July 23rd-30th 2011, Melbourne, Australia'''
  
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[[File:germination_stages.jpg]]
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Registration is open  [http://www.ibc2011.com/Dates.htm Important dates]  
  
 +
Symposium 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, will be held on Thursday, 27 July, from 1:30pm to 3:30pm.
  
 +
Dennis, Alejandra, Pankaj and Ramona are planning to attend.
  
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'''current: seedling growth:''' Growth of embryo after imbibition up to the development of the first adult leaves. part_of germination
+
See [[IBC 2011 Bio-Ontologies Symposium]] wiki page for more details
  
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Seedling growth stage should probably begin after germination, not after imbibition.
+
''PJ is staying at the Best Western. RW is staying at Hotel Enterprize. DWS is staying with a friend, and MAG has an apartment/suite nearby.''
  
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'''proposed:''' A vegetative growth phase that begins with germination and ends with the development of the first adult leaves.
 
  
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Comment: This terms is used only for seed plants, although non-seed plants may have a comparable phase during which they produce juvenile or transition leaves.
 
  
 +
* '''ICBO 2011  Second International Conference on Biomedical Ontology'''
 +
July 26-30,  2011
 +
Buffalo, New York  [http://icbo.buffalo.edu ICBO]
  
−
'''current: shoot emergence:''' Shoot or leaf breaks through the soil surface.
+
-LC will present the Plant Ontology on Thursday, July 28th, 3:40pm in the session:
 +
"Introduction to The OBO Foundry Initiative":  
  
−
'''proposed: shoot emergence phase:''' A vegetative growth phase that occurs when a shoot system emerges from a seed.
+
Also presenting will be: The Ontology for Biomedical Investigations,the Ontology for General Medical Sciences and the Infectious Disease Ontology.
 +
Link:  [http://icbo.buffalo.edu/2011ProgramTemplate.pdf ICBO Program]
  
 +
July 27 8.30am-4pm: LC is co-organizing the workshop [http://icbo.buffalo.edu/2011/WorkshopD.pdf "From Fins to Limbs to Leaves: Facilitating Anatomy Ontology Interoperability]
 +
along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.
  
−
current:
+
 +
* '''Plant Biology 2011, Aug 6-10th, Minneapolis, Minn'''
  
−
proposed:
+
[http://my.aspb.org/?page=Meetings_Annual Plant Biology 2011]
  
 +
Gramene and Plant Ontology are hosting a [http://outreach.gramene.org/gramene-outreach/index.php/ASPB_2011_Workshop Data Curation Workshop] again, focusing on pathway curations. 
  
−
current:
+
LC and PJ will present a [http://abstracts.aspb.org/pb2011/public/P21/P21013.html PO poster].
  
−
proposed:
+
TAIR (Kate Dreher) is organizing an [[Plant_Biology_2011_Outreach_Booth]] and we are invited to take part.  We are hosting the website.
  
  
−
current:
 
  
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proposed:
+
* '''POC Meeting at New York Botanic Garden'''  Tentative dates, Sept 9th-11th, 2011
  
 +
DWS will look into booking the apartments at the NYBG for accommodations.
  
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current:
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''We agreed that the PO meeting will be all day Saturday Sep. 10 and morning of Sunday Sep. 11.  DWS, PJ, BS, LC, and RW can make it. Need to find out if MAG can attend.''
  
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proposed:
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''RW has reserved the NYBG apartment for the nights of Sep. 9 and 10.''
  
 
=Next meeting scheduled for Tuesday, Aug 2nd, 2011 at 10am PDT/1pm EDT=
 
=Next meeting scheduled for Tuesday, Aug 2nd, 2011 at 10am PDT/1pm EDT=

Latest revision as of 19:37, 8 March 2012

POC meeting, Webex Conference Call; Date: Tuesday July 19th, 2011 10am (PDT)

In attendance:

POC members: Laurel Cooper (OSU), Ramona Walls (NYBG), Pankaj Jaiswal (OSU), Barry Smith (University at Buffalo, NY), Justin Elsner (OSU), Justin Preece (OSU)

Absent: Chris Mungall (Lawrence Berkeley National Lab), Dennis Stevenson (NYBG), Marie Alejandra Gandolfo (Cornell University)

Collaborators: none

Acceptance of the minutes from the POC_Conf._Call_7-12-11? There were no changes, additions, or deletions.


Tech Talk

A web service for PO terms

Justin Preece will demonstrate a prototype web service providing PO terms from the AmiGO database. This was originally built for his annotation wiki project, but could be expanded for general use and advertised as POC "technical outreach", to be consumed by other people's applications wanting to use PO data.

Example screenshots

JP and JE propose to add such a web service to plantontology.org.

For those interested in some technical background info: see Wikipedia's entries for web service, RESTful web services, and JSON.


JP: Purpose of these web services would include: data accessibility, potential to increase exposure of the PO to more users and application, technical outreach tool development

Questions: Do the keyword searches include synonyms? That should be possible if the terms are in the database

What about alternate spellings? add the British spellings in the synonym filed

Talk with the other groups at ICBO about how they deal with this issue.

Comments: BS shared a link with us to a Microsoft Word plugin that will give you a drop down list of terms from ontologies when you are writing a paper.

Update on the Translations:

details TBA...

JE has tested script for Japanese terms. Some problems putting them in alphabetical order, because it doesn't recognize UTF8 characters. Should work okay as long as there is only one synonym for each term (which is the case for Japanese synonyms).

Letter for OBO-Foundry acceptance

-PJ sent around a draft letter outlining the PO request for review:

Comments from BS:

  • Should go through list of OBO Foundry criteria. Order the points in the letter as the same order as the criteria.
  • Most important is proving a multiplicity of independent users. Not a problem for PO, but needs to be included.
  • Also should mention that PO is supporting tool development. Not in the OBO Foundry criteria, but will impress reviewers with good citizenship.
  • Need to make the discussion of the relations consistent- derives_from an experimental manipulations


See the associated page that LC created to gather the information for the OBO review : OBO_Foundry

Plant Physiology Publication

Comment on relations from BS (re. the letter and the paper): In RO, derives_from does not refer to manipulated material, but PO manuscript describes it that way. We should have a more specific relation for this. Need to see what others are using. Check with OBI.


RW:We have only been using develops_from for in vitro structures, but we did not necessarily mean to define it in terms of manipulations.

We reviewed the differences between transformation and derivation. Transformation is always one to one. Deriviation always involves a fusion or a fission. Classic example of transformation is zygote to embryo to child to adult. Example of derivation is zygote from egg cell and sperm cell.

Develops_from can be use when we don't know or don't want to specify if there is a transformation or derivation. This is not necessarily recommended, except that people really want to use it.

Transformation_of is a little vague, because there are underlying derivations that happen during a transformation (to the parts of the thing that is transforming). For this reason, develops_from might be better to use.

Talked about adding a new relation called "experimentally_derived_from" or maybe better "derived_from_by_manipulation.

Action items:

-Check with OBI to find out if they have a relation similar to what we need for in vitro structure.

-Rework the manuscript re. develops_from and derives_from so that is consistent with what we are doing.

-Be sure descriptions of relations in the OBO Foundry letter are consistent with the manuscript, and that all are accurate.


see additional notes in text below

Issues from last week's discussion

Use of develops_from and derives_from relations in PO

Last week we discussed how develops_from can be used to mean either transformation_of or derives_from.

From RO:

transformation_of: Relation between two classes, in which instances retain their identity yet change their classification by virtue of some kind of transformation.

And: ...one and the same continuant entity instantiates distinct classes at different times in virtue of phenotypic changes.

derives_from: Derivation on the instance level (*derives_from*) holds between distinct material continuants when one succeeds the other across a temporal divide in such a way that at least a biologically significant portion of the matter of the earlier continuant is inherited by the later.

And: ...from c derives_from c1 we can infer that c and c1 are not identical and that there is some instant of time t such that c1 exists only prior to and c only subsequent to t.


From http://www.berkeleybop.org/ontologies/obo-all/ro_proposed/ro_proposed.obo

id: OBO_REL:develops_from

alt_id: OBO_REL:0000038

name: develops_from

def: "A relation between two continuants, C and D. C develops_from D if C derived_from D or C transformation_of D. On the class level: C develops from D if and only if, for any x and any time t, the following holds: if x instantiates C at time t, then 1. either for some time t1, x instantiates D at t1 and t1 precedes t, and there is no time interval t2 such that x instantiates C at t2 and x instantiates D at t2 ; 2. or for some time t1 , there is some y such that y instantiates D at t1 and x derived_from y. On the instance level: x develops_from y is indistinguishable from x derives_from y" [GOC:cjm]

comment: Examples: eye develops_from eye disc; erythrocyte develops_from reticulocyte. Note that ontologies should use either derives_from or transformation_of where appropriate, but the develops_from relation can be used where one does not want to differentiate between these 2 cases

is_transitive: true

! domain: snap:IndependentContinuant

! range: snap:IndependentContinuant


We decided we needed to examine the instances of each of these relation in the PO on a case by case basis.

derives_from relations in PO:

lateral root primordium (PO:0000016) derives_from pericycle (PO:0006203) This one should be develops_from

leaf-derived cultured plant cell (PO:0000007) derives_from leaf (PO:0025034)

root-derived cultured plant cell (PO:0000008) derives_from root (PO:0009005)

change the latter two to something like derives_by_manipulation_from

develops_from relations in the PO:

See list of develops_from relation in PO 07-2011

participates_in relation

We use the participates_in relation to describe the whole plant growth phase in which an anatomical entity occurs. For example:

sporangium participates_in sporophyte phase.

There is no restriction on the participates_in relation that says that just because A participates_in B, it cannot also participate in C.

Saying sporangium participates_in sporophyte phase does not preclude the possibility of sporangium participates_in gametophyte phase (although of course it doesn't).

What we really want to say is sporangium participates_in_only sporophyte phase. Should we create a more specific relation to say this? This would be much more powerful for reasoning than the regular participates_in relation.

From CM (via email):

adding the only qualifier is easy in OWL, but not in OboEdit. Also, although we want to exclude structures from participating in other whole plant growth stages, we don't want to exclude them from participating in other processes (which the only qualifier would do).

In OWL, we cold say: sporangium SubClassOf participates_in only ('sporophyte phase' or not 'life cycle stage'

but this is difficult in OboEdit.

Chris recommends that we:

i. Create a shortcut relation called (OK, we need a better name here!) "participationally_disjoint_from".

ii. Add a macro expansion definition to this (tech. spec. is here: http://oboformat.googlecode.com/svn/trunk/doc/obo-syntax.html#7 -- but I can do this for you)

iii. Make direct triples between sporophyte and gametophyte in OE using this relation (note this is not an all-some relationship, it's a direct relationship at the class level. confused yet?)

which would be similar to creating an OWL axiom that says: (participates_in some sporophyte) DisjointWith (participates_in gametophyte)


This proposal is okay to use tentatively, but we should not go into too much detail about the participates_in relation in the current manuscript, because our usage of it may change as we rework the PGDSO. We can describe it more in the next manuscript.

We still need to use or mention participates_in in the paper, in order to say how we would describe a gametophyte or sporophyte, but don't make it a focus.

A sporophytes is a whole plant during the time it participates_in the sporophyte phase. We need a solution for this temporal issue.

Request from Cell Ontology (CL)

CL plans to obsolete most of its plant cell types, and add xrefs to those for PO terms.

CL will provide bridge files as part of the CL release process. An example of this is provided in the WOMBO paper (upcoming at IBCO).

PO has appropriate terms for all but four of the CL terms, although two of the terms are obsolete (PO:0000373 mucilage cell and PO:0000020 starch sheath cell).

four problematic terms

PO does not have equivalent terms for these CL terms, because it was set up for only angiosperms. Suggest we add terms like these when we work on the revisions of conducting tissue and cells. The CL terms come form Esau's Anatomy of Seed Plants. For now, Terry has removed the problematic xrefs from CL, will update them if we add new terms.

CL:0000399 phloem element (PO could add phloem element, similar to xylem element, parent to sieve element and phloem fiber)

CL:0000364 ray cell (PO has ray wood parenchyma, but ray cell could be parent to both ray wood parenchyma and ray tracheary element)

CL:0000294 sieve cell (could add this term for gymnosperms, if still used, see Esau)

CL:0000268 sieve element (PO has sieve tube member, but sieve element could be parent to both sieve tube member and sieve cell)

okay. we can contact them if we add terms for these.

epidermal cell

CM writes:

CL:0000362 ! epidermal cell [DEF: "An epithelial cell of the integument (the outer layer of an organism)."]

GO uses "epidermis" in this way. However, I would prefer something like:

integumental cell (functionally defined, lives in CL or FUNCARO)

epidermal cell (vertebrate sense, lives in CL)

plant epidermal cell (lives in PO with name "epidermal cell", imported into pan-euk view with obofoundry unique label "plant epidermal cell")


PJ would prefer that they just take the PO branch for plant cells and import it into the CL.

They still need to obosolete (or merge) their terms, so there are not duplicates.

We confirmed our decision last week that epidermal cell should be renamed "plant epidermal cell" When other ontologies import PO terms, they will have to remove "plant" from the name before appending "plant" to all of the PO term names.

We need to talk to CL about how they will link to PO terms. Lol will see Terry Meehan at ICBO meeting, and/or we could set up a phone meeting with them.

User requests, Plant Anatomy Ontology:

postponed until a future meeting- see POC_Conf._Call_8-2-11

Legume terms submitted by Austin Mast

phyllode

Maize GDB

transition leaf - definition

leaf base

style, silk, Poaceae style

Upcoming meetings 2011:

  • International Botanical Congress (IBC2011)

July 23rd-30th 2011, Melbourne, Australia

Registration is open Important dates

Symposium 'Bio-Ontologies for the Plant Sciences' under the Genetics, Genomics and Bioinformatics theme, will be held on Thursday, 27 July, from 1:30pm to 3:30pm.

Dennis, Alejandra, Pankaj and Ramona are planning to attend.

See IBC 2011 Bio-Ontologies Symposium wiki page for more details

PJ is staying at the Best Western. RW is staying at Hotel Enterprize. DWS is staying with a friend, and MAG has an apartment/suite nearby.


  • ICBO 2011 Second International Conference on Biomedical Ontology

July 26-30, 2011 Buffalo, New York ICBO

-LC will present the Plant Ontology on Thursday, July 28th, 3:40pm in the session: "Introduction to The OBO Foundry Initiative":

Also presenting will be: The Ontology for Biomedical Investigations,the Ontology for General Medical Sciences and the Infectious Disease Ontology. Link: ICBO Program

July 27 8.30am-4pm: LC is co-organizing the workshop "From Fins to Limbs to Leaves: Facilitating Anatomy Ontology Interoperability along with Melissa Haendel, Chris Mungall, Alan Ruttenberg, David Osumi-Sutherland.


  • Plant Biology 2011, Aug 6-10th, Minneapolis, Minn

Plant Biology 2011

Gramene and Plant Ontology are hosting a Data Curation Workshop again, focusing on pathway curations.

LC and PJ will present a PO poster.

TAIR (Kate Dreher) is organizing an Plant_Biology_2011_Outreach_Booth and we are invited to take part. We are hosting the website.


  • POC Meeting at New York Botanic Garden Tentative dates, Sept 9th-11th, 2011

DWS will look into booking the apartments at the NYBG for accommodations.

We agreed that the PO meeting will be all day Saturday Sep. 10 and morning of Sunday Sep. 11. DWS, PJ, BS, LC, and RW can make it. Need to find out if MAG can attend.

RW has reserved the NYBG apartment for the nights of Sep. 9 and 10.

Next meeting scheduled for Tuesday, Aug 2nd, 2011 at 10am PDT/1pm EDT

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