Conference calls Biomaterial 2007 notes

DetailedNotesJul6

Tina, Bjoern,Helen,Susanna,James, Alan Biomaterial Call notes: 06 July 2007 Terms now imported. Under bionmaterial, all terms and no structure BP:switch between truly biomaterial as in natural organism, bits, proteins and switch away experimental artefacts. Under natural then things that are not outr scope, but mapping works from here. HP:seems clean AR:all stuff in natural side should be mappable elsewhere org_part, organism, organism_status, in vivo biomaterial, Tina, thought we would split org status into a role. AA: split this, added as an editor note In parallel we do exp. artefact cell_pellet, biological macromolecule - defintion needs a tweak to define in natural suspension - intended to be the natural kind There are two organisms, difft OBI ids, is a bug. BP:could be an import error AR:could be was already there and got put in again. AA:resolve dupl. orgs AA. Population - to be decided if natural can include e.g. a KO or not AA.strain, same problem with inbred AR: natural, composite, or syntehtic - inbetween class could work. These are e.g.s of in betweeners. population. Emulsion same issues Ecotype - natural, mult inheritance possibly? PBS - experimental, not a biomaterial, BP:we have chebi objects HP:can be material, and biomaterial AR:redundancy? Cell, natural, - could be snythetic syn_polp -exp transgenic_organism, exp whole_mount - exp chebi objects solution serotype - natural genetic_modification - is it a thing or a process display_library - artifical lsyate - what about when get viral lysis? individual - problem haplotype - quality genotype - quality diplotype - quality, left alone, should have been in SO. BAL - exp cDNA - exp cell_supernatant - cohort - role biosourceprovider - role, organization serum, natural but getting it is experimental plasma, " organ_section " - alone, always an experimental artefact - AA. xenograft - new term, HP will define do offline AA. chimera - new term, HP will define do offline libray - exp liquid_chemical_solution allele - role unicellular_org - natural

BP:alternate grouping chemical soln, mol mixture,PBS, all are like definition of material some kind of aggregates, or composites. These can be exp or natural. SOme are pure parts e.g. chemicals, have that as an alternate split, mixtures, vs. unit SS:if under exp material, experimentally created or transformed material. PATO will have exp quality and also a natural quality SS:we can split the material from the biomaterial BP:don't know how to proceed now.. Not clear what Susanna said. is there a change we need to make SS:you wanted to split, is that correct? SS:split buffers vs. biological. AR:e.g. serum is that biological or experimental SS:exp, but is biological AR:but then is boh BP:natl vs exp might not be the best split. BP:soln, mol mix are the same kinds of things, group together with emulsion, suspension, liquid_chemical_soln and PBS. PBS is-a liquid chemical solution AA:there are 2 viruses in the OWL file. One needs removing Cell_culture - experimental AR:shall we group the parts of things - org part, org section SS:immortal cell under experimental Individual is this a synonym for organism. Is an identifier for an instance in an experimental setting. AR:genotype is a quality - HP:is notation for a mutation that is a variant of stuff AR:not saying that genotypes don't belong in single inheritance fit in pATO HP:needs to be biologically useful, single inheritance isn't how biology works BP:can it be on a gene or a whole genome? AR:needs to considered by whole branch BP:put a new group genetic information content, allele, genotype etc gop under it. HP:in any case we need a mapping to these things even if not in OBI BP:organisms, genes etc have GeneticInformation and these are children of genetic information AA:individual - now needs to be under to be discussed. organism_status - pre-mortem, post-mortem, - that's an organism quality. BP:could be going in sample annotation SS:alive and dead are qualities in pato - HP:keep org_status - that needs to come from pato need a mapping point AR:can define classes as defined classes, live organisms, defined class of organism and pato quality alive. TB:Susanna are you planning to present the problems? SS:missed that, was focussing on the open part TB:rbinging up the discussion points useful, where we are in the branch, what we want to bring up at the workshop. Tues am. Agenda - update of development status for branches HP:suggest we at least talk about the branches. SS:we could point at specific problems we have been encountering TB:genetic info content - e.g. discuss what we need etc, BS will have an opinionl. Better to hear this earlier. SS:apart from tbe genetic terms, HP:synthetic vs natural, that this is not clean BP:mention the protocol application things. cell line, cell culture - linkage between process and material - passage no, org from which cell line was derived. Interbranch relationships. HP:should we stop at this point BP:not happy with the structure, people will tear it apart. Either don't look at structure, or we spend some more time on this. SS:if you agree, I suggest to bring the file up, and asy is preliminary, bring up these and fill it in. Hp:Bjoern if you have ideas do it. I will see if I can motivate Alan. BP will arrive on Weds am. AR: will be there on Sunday night. AR and BP want to strcuture it some more. AR hoping would be some slots of work time to do things there. BP;may send an email of high order structure that I would like. AR:I can also send some notes. AA:put OBi ids, and check in. HP:If I send the defs this pm can you put them in? AR:yes.

DetailedNotes28Jun

Detailed BioMaterial Call Notes 28 June 2007 Bjoern Peters, Tina Boussard, Alan Ruttenberg, Susanna Sanonse, James Malone, Helen Parkinson. Biomaterial Call BP, Alan did you edit the working version? Were those yours? AR:not made edits to the google docs BP:did someone modify on the call? Anyway I started from it and I have a final version, and I have added that. BP:goal was to provide the OWL file, got files from Susanna, Jennifer's file wasn't quite what wanted SS:I reposted what she sent BP:Not in shape that we can post it HP:should have happened that we sent this BP:Start with JF_final Line 6 - SS will edit the doc while we talk. Many are qualities, some are horrible BP:Want to go through this AR:suggest a col where could go. HP:suggest that we add a col and say out scope, let Jennifer sort these SS:where;s immortalized? BP:immortalized cell was in sheet SS:was discussing fix cells, and could go in PATO - exp created quality - could have a different root in PATO BP:immortalized is in, as cancer cells not nec exp BP:Primary - HP: in CTO? AA:to check if primary etc are in HP:what is a cell strain? BP: I had cell strain, why duplication SS:def and source the same. She has all the CEBS, she's the right person to do that BP:Cell strain - is like where they are derived from, is covered BP:do we have org strain anywhere? TB:has org strain, AR:is a subclass BP:we need to add strain specific terms AR:strain rather than organism, or cell BP:we need this Alan is it OK for organism strain AR:personal favour for BP OK AA:we added it and we'll come back to it FetalStatus - should not be included at all by this definition Death status, remove. AR:it;s clear what she's doing here, and we need a cookbook for translate into OBI. She's reflecting her data model. HP:this has been an ongoing problem with CEBS. More productive here to map to all repositories HP:Organ_section - we have organ part - this covers it. Is this a section provided by a process. Parts of organs and parts of organisms - BP:organism_section made by sectioning AR:is a defined term HP:whole_mount ? BP:org sample prep as a process AR:is an aggregate, and not the whole thing is not a part BP:is a former part for section. Organ_part is in scope. We need a general term that includes whole org prep and whole_organism - BP - crap, typically needed. HP:retain whole_org as a synonym Cell pellet we keep - process, supernatant - we have cell supernatant SS:specimen_pool - no. HP:checked population, did Susanna have mixture? SS:mixture - had a type of - should have a parent mixture HP:we've learned learn that the sheet should have been merged and these terms checked before sending to Bjoern AR:what does a mixture of specimens need? HP:I will do the things in scope for Jennifer. BP:Susanna's sheet nothing to discuss BP:final version Rows 3-16. Biomaterial term lis goes to other branches Final sheet, liquid chemical sol, changed purely that editor things for myself, and there's no source, we can add or remove as needed. Added a few examples. I merged one or two terms, that were the same by 2 communities HP:question re merging? BP: artificially_engineered_material and construct - bad primary class name - HP:did these get remained as synomyms. BP:in case of virus, was identical HP:just a point about retaining synomyms in general to allow back mapping later BP:also moved comments to editor notes HP:any probs that want to look at? 19. protein_fragment - AR:part of a protein? BP:not if I make it AR:name is bad should be synthetic peptide, and def is bad BP:not sure about this, not only when synthesize it- might detect it in e.g. mass spec - peptide vs protein ? HP:if it;s 40 with posttranslational modifications, is it still a peptide? AR:def doesn't make it clear but is in scope BP:peptide vs. protein fragment are synonyms here AR:detect by mass spec BP:when refer to something 'part of protein' derived from protein, or made it yourself HP:if you made it then it's an artificially engineered biomaterial BP:want to link to a say it's an enzyme - and want to say it's synthetic HP:to say it's an enzyme is a catalytic siet BP:want to say it's same function as whole protein as AR:that's different - statement for a function HP:is this a proxy_for? No. AR;peptide may have same function as the protein BP:gave a bad e.g. was supposed to linlk partial sequence of whole protein, or synth or detect now want to say can be derived from a whole protein - 'derived -from' AR:if not derived from, or synth should be part of the same class HP: I would split them AR:agree, natl products not in scope of OBI SS:we have constructed from, different from derived_from BP:consenus to split, maybe merge later - hard to disinguish between synth and natural side by side AA:synthetic or nat occuring not something easy to split and often used side by side. SS:also what happened in pato - natural and artficial will be separated. AR:no need to split it - synthetic vs derived from natural usage model determibe whether we have 2 classes. BP:puts in synth polypeptide as a child of artifically_engineered_material Natural one is derived from protein - may not be a class - BP:fragment_derived_from protein - same def as before pretty much. All done for BP's sheet. All other terms OK and in original intent. May be discussions later ob SS:In othr sheet, are these in the dispatcher file, OK? BP:Will upload my version of this file. SS:I can help next week putting into protege. HP:to provide terms in same format as the final sheet. SS:we could structure it next week in protege HP:will try and do this pm, depends if Susanna can get the notes out tonight JM:batchloader works now. AR:leaves.

DetailedNotesJun22

BioMaterial Call Bjoern, Alan, Philippe, Trish, Tina, James, Susanna, Helen Sarting with Susanna's terms, probs in yellow fixed_cell - PATO - fixed quality in PATO? purified - also checking with PATO? need a process for purification living cell - alive is in PATO, cell - root node for cell type Discussion woth Chris and George, suggest we keep compound terms, and they keep the atomic. Bit confusing. TW:Are OBO compound terms, are these cross product? Yes apparently, In OBO they allow cross products, in OWL these can be build up with necessary and sufficient. AR:As no formal reln on OBO they called it cross products, not so in OBI, so we can do with OWL Questions on: Solid, gas, liquid, - PATO - solidity/gaseous. We also need to record that there is a GAS. Need to make reln between what is solid, e.g. water. DO we need this in OB AR No BP:yes PRS:in cell culture, specifcy the gases, or proportion of gases TW:need to specify the compound, and then say what the state is AR:there will be parts of the environment Discussion on whether the gas itself is needed. AR:we need gas and substance, we should change the definition. BP:Qu - gas, liquid, solid, - dofft way of slpiting the hierarchy different from how chebi would do. What types of high level nodes do we need. AR:will lead to mult inheritance BP:yes, but we want to get the high level nodes and limit taht we don't include blood SS:thing right, the def by PSI - all tehy want to do is id the state - sample is liquid - PATO quality sufficinent. AND we may need to say this is a gas. If we only need to do what PSI want - then this is fine. Happy to do that. AR:let someone resubmit the term if they really want it. Susanna has no more questions on her terms. SS:looking at the dispatcher file? HP:has anyone else we got defs for terms we care about PRS:molecular mixture - puzzled. A combination of two or more compounds. Def prepared by MO, was about related. AA:HP to check on the original MO use of mixture PRS:solution, got roles, solute, solvent - these need to go to role Susanna, talked about substance, not chemical, need to cross check TB:got PBS - role, and material SS:we need to review these to see if they are consistent BP:we seem to have duplicates as well PRS:PBS - 4 components, proportions, id solutes and solvents - lot of work for dealing with PBS. This is the way to go. There's a more grabnular model and then gfrab PBNS after it's classified TB;salmon sperm - biological fluid - DNA carrier - is a role. PRS:salmon sperm - species plus organism part and plus role - DNA carrier TB:status - alive/dead - PATO TB:org_part - part of the organisms anatomy or derived from biomaterial HP:think I would split into what's a part and what's derived BP:looking forward to high level structure SS:in dispatcher term, some terms not assigned to branches, or external. back to checking these. BP:sequence ontology workshop, all taken care in SO. All the parts of antigenic molecules SS:ions, 41-43 - from PSI and chebi etc. PSI was not to submit all now. Wanted to plug in later. SS:branch terms, we need to assign people to taking these to other branches AA AR:takes reln branch terms SS will note these into a file. AA TW:will take instrument branch terms AA SS: will senf to Jennider AA SS:cell line ontology will do AA TB:disease ontology AA: AR suggests send CARO to Chris M Discussion on need for follow up and what to give to other branches and what the workload to do this is. PRS: I put on the google all the PATO SS: I am not using the google. PRS: I did all the mapping to all the other ontologies SS: so is this file out of date PRS: I checked which terms were in unit, pato, cell line etc BP: add to status SS:also the current file has, need to check which is more up to date, Reason to assign to diff branches is to deal with one person does it and fields the question. AR:we are middle men and we maybe should be refering to the originator TB:but that person doesn't know history BP:needs to be us who does it, not easy TB:we need to send them out so we at least move forard. AA: PRS/AA will make one single dispatcher file AA: Philippe to send aroung the link info, and check the google account email and link to the google calendar AR:leaves TB:leaves SS:suggest that we assign an editor BP:agree, but priorities need to be elsewhere. Clear that for my time want to work no on dispatcher files. PRS:cam we go back to defs SS:we agreed to do this onwly where there are problems BP:will do the OBI OWL file, need to remove redundancy, needs def and example and seems to still be redundant. AA:all to clean up the files for Bjoern HP:in the google files or not? TW: if mult people are editing then googkle better HP:what's your preference Bjoern BP:need it in a week. Suggest we use a wiki for that. Next Wednesday deadline for these - 29th AA: all to send cleaned up list of terms with def and with example by Weds next week 27 June. SS:want a structure? BP:no need, easier to do in OWL SS:simply full list of terms then BP: asks Trish, way for us to look at protege file via centra. TW:GF invited all branch leaders to centra TW:ignore date, all people on email can be a presented. BP:should try on centra AA:all install centra which now supprts macs - need to preinstall for macs to use next week. TW:is a standing meeting, so can log in at any time.

Describe DetailedNotesJune8 here.

Helen, James, Bjoern Susanna will edit the file if there are call comments and will save it again. 1. Allele - recessive - HP will look these up in PATO George 2. biomaterial_purity - HP to check with George, agree with generic

BP do we have a good definition of what biomaterial is vs. material 'Any material in scope is a biomaterial and is in scope' better definition needed then for material and biomaterial BioMetrics - removed OrganismPart now includes cell BP agrees. Question on whether has to be in part of the whole? BP requires this HP:could be either in my view HP:take point - 3 cases - hand/arm example BP:can consider work with as part of the organism and then quality for derived from, - or call it sample, and then sample 'derived from tail' HP:cell_lysate - are there other types of lysate -> lysate term. SS:didn't thinkabout removing cell, also found sub classes - whole lysate, cell free lysate. AA:SS will put these on her sheet. BP:did we submit lysing to process - might be useful. BP:two typos on rows 13 and 15. HP:that's all the comments I had. BP:didn't do the others right. And lots of redundancy HP:is there anything else on the agenda SS:have two terms, not problems, looking for possible subclass- lipid emulsion - dispersed phase vs., continuous phase. Should we get the possible child terms. HP:good to make a note of these terms. PRS:looked at cell lysate and extract in group 4 should all be grouped BP:I thought I had all the cell terms SS:was supposed to be BP:we can merge them. HP:mult people doing defintions doesn't hurt BP:did we id any relations> HP:the one that you just mentioned 'derived_from'. Is this generic - e.g. derives from an organism or data from data. BP:was defined originally for developmental biology PRS:what are the bearers of the relation, continuant and processes? E.g. structure - can something derive from a process? BP:materialTransformation in P/A haev output derived from input Sampl outout cellsep process, imput is tail of a mouse - tail of a mouse was derived from the mouse. PRS:do we need a type - derives from a process HP:these are subtypes of derives from PRS:process/continuant bearers could be different BP:hoping could work with a single derived from relationship AA:PRS will post qu to the relation branch about this SS:request on ProtocolApplication page example on branch page would be good, even if is text BP:on P/A branch still not in good shape BP:shows proxy_for relationships - in the processes - measuring cell killing - really measuring radioactivity HP:don't find this useful - al science is an artefact

BP:I believe the cell culture is T cells, work at level that is X tube, with x media HP:don't get the point, BP:biomaterial is a cell culture for 4 weeks, missing the point that the sample is a tumour in the patient so that can relate these things together. Proxy for is sim to derived cells, HP:how is that different from derived from - BP:always derived from, proxy for gives you something extra - tells you that you believe is there. HP:unconvinced. SS:if it works, then we can use it. SS:we are 30 mins in, unless people have other things, suggest we do the rest o of the terms JM:on dt call we will create a doc similar to the one Daniel did. SS:open to a way that we can report to the group BP:good idea to do that could do before the call JM:also summary of what has been done etc. SS:happy to do before the call. HP:could we do that well before the call please. SS:will circulate on Monday 18th June before 20th/ SS:if you want to keep editing this file Helen then you are leading editor of this file. SS:Tina and Philippe were happy to get terms. HP:If Jennifer can't do hers then we need to know asap. Philippe gets: environmental_sample - mol mixture Tina: Organism through whole organism. Both to edit the sheet.

DetailedNotes

Describe DetailedNotes here. Complete Notes for BioMaterial Branch call 1 June 2007 Present: Helen, Susanna, Bjoern, Tina, Summary: 1. We will divide up the biomaterial file and assign rows by source or choice to people. - Susanna will do this and post. People will get what they submitted where possible. 2. BP wants lines 85-93, 53, 38-39, 82-83, 34, 16 3. We will each do defs, suggest a class 4. These will then be reviewed on subsequent calls esp. if problematic - non contentious things need not be discussed first 5. Aim to have a sheet with defs, classes etc and hierarchy to make an OWL file by the workshop.

Susanna explained how dt group had divided by rows, assigned to people, review defs and suggest heirarchy, harmonise to naming conventions. How does this sound to the others. Susanna, Bjoern what do you think? Can we do it all on the call? BP:would really like to do it all on the call. SS:only 5 calls till the workshop BP:throught main point was to do an OWL heirarchy, need to do relative to each other TB:is working for dt at least BP:adv of moving to OWL there's at least something SS:hard to do things in the OWL file BP;do we have a google file SS:not yet, no password Philippe is not here BP:worked well for P/App, sent to mailing list and all could see it SS:will sort out for next week. BP:should focus on the hierarchy in the calls We agree. HP:suggest sort by source for the assignment BP:we sorted already - we need to resolve the redundancy though HP:yes TB:all terms next to each other, will need to merge these Look at the source, if terms identical from one source then will be assigned to each other BP:if something not clear then dumpt it for now. MO/CEBS/IED/PSI/MIACA etc MO/AE - Helen IED - Bjoern CEBS - Jen PSI - Susanna PharmGKB - Tina will also review in second round other's definition HP:should generate a std format for a definition e.g. for dt we have data in, data out -> example HP:min case we already need an example, an example is like an instance or child concept of the class

AA:All to post the files that we have done. HP:SUggest that we make a small table to show these SS:re dispatcher files - when we submit these are we as OBI? HP:yes for SO terms that James did SS:we should be able to do the terms to other resources and get through the terms in 5 weeks BP:Can we do this by next week? SS:review the terms and put in hierarchy? SS:aim to get all the definitions by next week is the aim TB:for dt - everyone did their defs and we only talked about things that were straighforward SS:implies that we should read the definitions by the call? TB:yes SS:we will take a couple of calls to get through these BP:want to get to OWL SS:do you want to on SS or in OWL, my view is on SS BP:only concern is that we do the hierarchy even if on s/sheet SS:if we agree then for the final call we can do it OWL BP:from protocol application we need the owl file - as we need relns to cells for e.g. cell_sorting SS:will be hard to understand what each branch has done, then at workshop we can do that at the workshop BP:P/appl though is defined by other things. SS:OK we will do our best then - BP is volunteered to create the OWL file. SS:anything else to discuss? BP:Assignment of terms - shall we go through now. SS:will do when I sort BP:assigned the following 85-93, 53, 38-39, 82-83, 34, 16

SS:do want also the IED, transgenic_organism BP:this is a mess, 53-54, 107-108 some redundancy still. SS:will deal with these. We can always have mult definitions. HP:helps to have people to bounce these off encourage people to mail each other.