hemopoiesis

[gocentral]

We've received email on GO process terms dealing with hemopoiesis (GO:0030097 and children); it looks like that area needs an overhaul.

For background, what GO has now is based on what a decided non-expert (me) gleaned from Gilbert's Developmental Biology text, so it makes sense that someone in the field would be able to do a lot better.

Send email to the GO list with proposed changes, and cc David States in case he isn't on the list or monitoring this SourceForge entry. This is what he sent to the list; it contains lots of useful suggestions:

Date: Sun, 26 Jan 2003 16:52:14 -0500 From: David States <dstates@bioinformatics.med.umich.edu> To: go@genome.stanford.edu Subject: Hemopoesisis issues

Hi,

Was recently looking at the GO terms related to blood formation, and I am not sure that I agree with the structure of the current ontology. Specifically:

Hemopoeisis GO:0030097 is divided into

• hemocyte development GO:0007516
• lymphocyte development GO:0030098
• myeloid cell development GO:0030099

1) Where is the "erythroid cell development" category? In vertebrates, this is quantitatively the dominant lineage and clearly of great biological importance.

2) Many of us regard hemocytes and myeloid cells as homologous (1,2). Rather than separate GO classes, should not they be merged into a single class?

3) Platelet formation GO:0030220 and megakaryocyte differentiation GO:0030219 are both listed as children of myeloid development, but platelets form by budding off megakaryocytes so should not platelet formation be a child of megakaryocyte differentiation? Further, it is generally accepted that the megakaryocyte lineage is a branch off the erythroid lineage (3), and hematologists would regard classifying megakaryocyte differentiation under myeloid development as an error.

David

1) Lebestky T, Chang T, Hartenstein V, Banerjee U. Specification of Drosophila hematopoietic lineage by conserved transcription factors. Science. 2000 Apr 7;288(5463):146-9.

2) Fossett N, Schulz RA. Functional conservation of hematopoietic factors in Drosophila and vertebrates. Differentiation. 2001 Dec;69(2-3):83-90.

3) Williams Hematology, McGrawHill 2001 ISBN, 0070703868

David J. States, M.D., Ph.D. Professor of Human Genetics Director of Bioinformatics University of Michigan School of Medicine Medical Science Building I, Room 5443 Ann Arbor, MI 48109 USA email: dstates@umich.edu tel: (734) 615-8895 fax: (734) 615-6553 URL: http://stateslab.bioinformatics.med.umich.edu

Reported by: mah11

Original Ticket: "geneontology/ontology-requests/645":https://sourceforge.net/p/geneontology/ontology-requests/645

[gocentral]

Logged In: YES user_id=451873

I'm trying to revise the 'hemopoiesis' node of the process ontology in response to David States comments, and this is what I've come up with. David and Tanya, if you could take a look because they're all development terms. This is what we have now:

hemopoiesis ; GO:0030097 ---%hemocyte development ; GO:0007516 -------<hemocyte differentiation ; GO:0042386 ---%lymphocytic blood cell differentiation ; GO:0030098 ---%myeloid blood cell differentiation ; GO:0030099 -------%megakaryocyte differentiation ; GO:0030219 -------%platelet formation ; GO:0030220

These are the changes I'm proposing:

1/ Merge hemocyte differentiation ; GO:0042386 into myeloid blood cell differentiation ; GO:0030099 (added appropriate synonyms).

2/ Change 'hemocyte' to 'myeloid blood cell' in all term names (add synonyms)

3/ Made myeloid blood cell development ; GO:0007516 a part_of child of myeloid blood cell differentiation ; GO:0030099, as per the rules we set at the meeting.

4/ Add new term erythroid cell differentiation ; GO:new

5/ Move megakaryocyte differentiation ; GO:0030219 under erythroid cell differentiation ; GO:new.

6/ platelet formation ; GO:0030220 to go under either megakaryocyte differentiation ; GO:0030219 (part_of) or erythroid cell differentiation ; GO:new (is_a). Platelets are formed from megakaryocytes, but don't know if that counts as being part_of megakaryocyte differentiation or not.

New structure:

hemopoiesis ; GO:0030097 ---%myeloid blood cell differentiation ; GO:0030099 synonym:hemocyte differentiation ------<myeloid blood cell development ; GO:0007516 synonym:hemocyte development ------%plasmatocyte differentiation ; GO:0042387 ------<regulation of myeloid blood cell differentiation ; GO:0045610 ---%lymphocytic blood cell differentiation ; GO:0030098 ---%erythroid cell differentiation ; GO:new synonym:red blood cell differentiation ------%megakaryocyte differentiation ; GO:0030219 ---------<platelet formation ; GO:0030220 OR ------%platelet formation ; GO:0030220

Original comment by: jl242

[gocentral]

• milestone: --> TermGenie
• assigned_to: nobody --> jl242

Original comment by: jl242

[gocentral]

Logged In: YES user_id=482748

Based on some emails to the hemopoeisis interest grp (summarised in SF:912824), I've made some edits to the hemopoesis section that will affect this SF entry.

1. Have added 'sensu Arthropoda' to any process terms containing 'hemocyte'. This distinguishes the arthropod hemocytes (a general term for arthropod blood cells) from vertebrate ones.

Therefore 'hemocyte' should not be changed to 'myeloid blood cell' in all term names, and hemocyte differentiation (sensu Arthropoda) ; GO:0042386 shouldn't be merged into myeloid blood cell differentiation ; GO:0030099.

If wanted, 'hemocyte differentiation (sensu Vertebrata?) could be added as a synonym for GO:0030099.

2. I have already moved hemocyte development (sensu Arthropoda) ; GO:0007516 to be a child of hemocyte differentiation (sensu Arthropoda) ; GO:0042386.

Therefore, all that is left to be done is steps 4/ - 6/ (adding a 'erythroid cell differentiation' term and checking the parentage of 'megakarocyte differentiation' and 'platelet formation').

Becky

Original comment by: beckyfoulger

[gocentral]

• assigned_to: jl242 --> jenclark

Original comment by: jenclark

[gocentral]

Logged In: YES user_id=865072

Hi Jen and other interested parties,

Having attempted to figure out the logic of steps 4-6 of Jane's plan below versus what we have already in the GO versus published reviews, I must admit I really think that none of these steps are appropriate.

"4/ Add new term erythroid cell differentiation ; GO:new"

The impetus for this term based on the phrase "erythroid cell" seems to have been the use of the phrase in a single line of a David States email.
"Erythroid cells" are erythrocytes -- we already have GO:0030218 erythrocyte differentiation. One could argue erythroid cells also encompass committed progenitors of erythrocytes, but such cells types are included in the definition of GO:0030218 and no separate term is needed.

5/ Move megakaryocyte differentiation ; GO:0030219 under erythroid cell differentiation ; GO:new

I disagree with this. megakaryocytes and erythrocytes arise from a common progenitor, see PMID:12615892 or PMID: 12615892, for instance.
Making megakaryocyte differentiation a type of erythrocyte differentiation would suggest that megakaryocytes are somehow a specialized type of erythrocytes, when in fact the two cell types have very distinct structures and functions.

6/ platelet formation ; GO:0030220 to go under either megakaryocyte differentiation ; GO:0030219 (part_of) or erythroid cell differentiation ; GO:new (is_a). Platelets are formed from megakaryocytes, but don't know if that counts as being part_of megakaryocyte differentiation or not.

GO:0030220 platelet formation is an odd bird indeed. Platelets are not actually cells, although they are membrane-bound and have a limited amount of metabolic machinery, although not for instance, protein synthesis, and have no nucleus. They bud from megakaryocyte membrane extrusions, but do not differentiate following their budding.
They are not a type of megakarycyte, or of any cell, because they are not cells.

Platelet formation is really a type of vesicular body secretion by cells, and should be grouped with similar terms, such as the membrane viral budding terms (which ought to be collected under a single "viral membrane budding" grouping term), exosome formation (we don't have a term for this, but we should; exosome is a term for secreted vesicles released from various cell types and having functions in signaling and immune activation), and blebbing or budding of apoptotic cells (see PMID:15699075 for evidence that this is a regulated process).

Perhaps I will work up a SF item based on this thought, but for the moment, I would recommend that GO:0030220 platelet formation remain where it is.

All in all I would recommend that this SF item be closed with no further action.

-- Alex

Original comment by: addiehl

[gocentral]

Logged In: YES user_id=865072

Hi Jen and other interested parties,

Having attempted to figure out the logic of steps 4-6 of Jane's plan below versus what we have already in the GO versus published reviews, I must admit I really think that none of these steps are appropriate.

"4/ Add new term erythroid cell differentiation ; GO:new"

The impetus for this term based on the phrase "erythroid cell" seems to have been the use of the phrase in a single line of a David States email.
"Erythroid cells" are erythrocytes -- we already have GO:0030218 erythrocyte differentiation. One could argue erythroid cells also encompass committed progenitors of erythrocytes, but such cells types are included in the definition of GO:0030218 and no separate term is needed.

5/ Move megakaryocyte differentiation ; GO:0030219 under erythroid cell differentiation ; GO:new

I disagree with this. megakaryocytes and erythrocytes arise from a common progenitor, see PMID:12615892 or PMID: 12615892, for instance.
Making megakaryocyte differentiation a type of erythrocyte differentiation would suggest that megakaryocytes are somehow a specialized type of erythrocytes, when in fact the two cell types have very distinct structures and functions.

6/ platelet formation ; GO:0030220 to go under either megakaryocyte differentiation ; GO:0030219 (part_of) or erythroid cell differentiation ; GO:new (is_a). Platelets are formed from megakaryocytes, but don't know if that counts as being part_of megakaryocyte differentiation or not.

GO:0030220 platelet formation is an odd bird indeed. Platelets are not actually cells, although they are membrane-bound and have a limited amount of metabolic machinery, although not for instance, protein synthesis, and have no nucleus. They bud from megakaryocyte membrane extrusions, but do not differentiate following their budding.
They are not a type of megakarycyte, or of any cell, because they are not cells.

Platelet formation is really a type of vesicular body secretion by cells, and should be grouped with similar terms, such as the membrane viral budding terms (which ought to be collected under a single "viral membrane budding" grouping term), exosome formation (we don't have a term for this, but we should; exosome is a term for secreted vesicles released from various cell types and having functions in signaling and immune activation), and blebbing or budding of apoptotic cells (see PMID:15699075 for evidence that this is a regulated process).

Perhaps I will work up a SF item based on this thought, but for the moment, I would recommend that GO:0030220 platelet formation remain where it is.

All in all I would recommend that this SF item be closed with no further action.

-- Alex

Original comment by: addiehl

[gocentral]

Logged In: YES user_id=735846

Hi Alex,

Thanks for that. If you want to open a new item on platelet formation sometime then we will act on that, but I will close this item as you suggest.

Thanks,

Jen

Original comment by: jenclark

[gocentral]

• status: open --> closed-fixed

Original comment by: jenclark